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A SUPERTREE of BIRDS Katie E. Davis

A SUPERTREE of BIRDS Katie E. Davis

REWEAVING THE TAPESTRY: A SUPERTREE OF

Katie E. Davis

Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy to the University of Glasgow, Division of Environmental and Evolutionary Biology, January 2008

© K. E. Davis 2008 Declaration

I attest that:

All material presented in this document was compiled and written by myself unless otherwise acknowledged. Part of the material included in this thesis is being prepared for submission in co-authorship with others:

• Chapter 2: Davis, K. E. and Dyke, G. J. In Prep for Neues Jahrbuch für Geologie und Paläontologie . “Two new specimens of Primobucco (Aves: ) from the of North America”. K. E. D. carried out the descriptive work, phylogenetic analyses and wrote the manuscript. G. J. D. provided the specimens and advised on description and writing of the manuscript. • Chapter 6: Lloyd, G. T., Davis, K. E., Pisani, D., Tarver, J. E., Ruta, M., Sakamoto, M., Hone, D. W. E., Jennings, J., Benton, M. J. In Prep for Proceedings of the National Academy of Sciences. “ and the Terrestrial Revolution”. KED and GTL designed the data collection protocols. GTL, JET, MS, DWEH and RJ performed data collection and entry. KED and DP created the MRP matrices. DP ran tree searches, performed post hoc taxon pruning and produced support values. MJB and GTL collected the stratigraphic data and GTL performed the subsampling tests and calculated diversification rates. JET, MR and GTL performed the time-slicing and diversification shift analyses. MJB, GTL, JET, DP, MR and KED wrote the paper. GTL and JET produced the Supporting Information and Figures.

KATIE E. DAVIS, 2008

i Acknowledgements

I would like to thank first of all my supervisor, Rod Page, for his help and assistance over the years and also the other members of the Page Lab for help, encouragement and, at times, much hilarity. Thanks go to Matt Yoder, Peter Foster and George Sangster for contributing to the work in Chapter 4 by joining in with the Supertree Project. Matt Yoder uploaded trees, while Peter Foster and George Sangster helpfully pointed out data errors and synonyms. The results of that chapter are much improved for their input. I would also like to thank Gareth Dyke for his collaboration and advice on Chapter 2, and Graeme Lloyd, a friend and colleague with whom I worked on Chapter 6. Thanks, of course, also to the other collaborators on the supertree project. I would also like to thank NERC for almost giving me enough money to survive on for the last four years. My colleagues and friends Nadia Anwar, Helen Ablitt and Heather Forbes also deserve many thanks for their support and friendship over the last four years. Heather in particular has made the hard times so much more bearable and the good times really good. Finally, thanks go to my husband Jon. On a practical note he wrote the Perl scripts utilised so many times in this thesis, but more importantly has always been there for me and never complained once even when asked on numerous occasions to proofread chapters at unsociable hours of the morning (and still turned up to the wedding).

Katie Davis, 2008.

ii Abstract Supertrees are a useful method of constructing large-scale phylogenies by assembling numerous smaller phylogenies that have some, but not necessarily all, taxa in common. Birds are an obvious candidate for supertree construction as they are the most abundant land vertebrates on the planet and no comprehensive phylogeny of both extinct and extant currently exists. In to construct supertrees, primary analysis of characters is required. One such study, presented here, describes two new partial specimens belonging to the Primobucconidae from the Green River Formation of Wyoming (USA), which were assigned to the species Primobucco mcgrewi . Although incomplete, these specimens had preserved anatomical features not seen in other material. An attempt to further constrain their phylogenetic position was inconclusive, showing only that the Primobucconidae belong in a clade containing the extant Coraciiformes and related taxa. Over 700 such studies were used to construct a species-level supertree of Aves containing over 5000 taxa. The resulting tree shows the relationships between the main avian groups, with only a few novel clades, some of which can be explained by a lack of information regarding those taxa. The tree was constructed using a strict protocol which ensures robust, accurate and efficient data collection and processing; extending previous work by other authors. Before creating the species-level supertree the protocol was tested on the order in order to determine the most efficient method of removing non-independent data. It was found that combining non-independent source trees via a “mini-supertree” analysis produced results more consistent with the input source data and, in addition, significantly reduced computational load. Another method for constructing large-scale trees is via a supermatrix, which is constructed from primary data collated into a single, large matrix. A molecular-only tree was constructed using both supertree and supermatrix methods, from the same data, again of the order Galliformes. Both methods performed equally as well in producing trees that fit the source data. The two methods could be considered complementary rather than conflicting as the supertree took a long time to construct but was very quick to calculate, but the supermatrix took longer to calculate, but was quicker to construct. Dependent upon the data at hand and the other factors involved, the choice of which method to use appears, from this small study, to be of little consequence. Finally an updated species-level supertree of the Dinosauria was also constructed and used to look at diversification rates in order to elucidate the “Cretaceous explosion of terrestrial life”. Results from this study show that this apparent burst in diversity at the end of the Cretaceous is a sampling artefact and in fact, dinosaurs show most of their major diversification shifts in the first third of their history.

iii Table of Contents

DECLARATION ...... I ACKNOWLEDGEMENTS ...... II ABSTRACT ...... III LIST OF FIGURES ...... VI LIST OF TABLES ...... IX

CHAPTER 1 ...... 1

1.1 INTRODUCTION ...... 1 1.2 CONSTRUCTING LARGE -SCALE PHYLOGENIES ...... 3 1.3 SUPERTREE METHODS ...... 5 1.4 CURRENT ESTIMATES OF AVIAN PHYLOGENY ...... 10 1.5 THIS THESIS ...... 19 1.6 THESIS SUMMARY ...... 20

CHAPTER 2 ...... 22

2.1 ABSTRACT ...... 22 2.2 INTRODUCTION ...... 22 2.3 SYSTEMATIC PALAEONTOLOGY ...... 24 2.4 PHYLOGENETIC ANALYSIS ...... 30 2.5 RESULTS ...... 30 2.6 DISCUSSION ...... 32

CHAPTER 3 ...... 34

3.1 ABSTRACT ...... 34 3.2 INTRODUCTION ...... 34 3.3 CURRENT SUPERTREE BUILDING PROTOCOL ...... 35 3.4 METHODS ...... 41 3.5 ANALYSIS ...... 55 3.6 RESULTS ...... 56 3.7 DISCUSSION ...... 62 3.8 CONCLUSIONS ...... 63

CHAPTER 4 ...... 65

4.1 ABSTRACT ...... 65 4.2 INTRODUCTION ...... 65 4.3 METHODS ...... 67 4.4 RESULTS ...... 70 4.5 DISCUSSION ...... 80 4.6 CONCLUSIONS ...... 82

iv CHAPTER 5 ...... 83

5.1 ABSTRACT ...... 83 5.2 INTRODUCTION ...... 83 5.3 METHODS ...... 87 5.4 RESULTS ...... 91 5.5 DISCUSSION ...... 99 5.6 CONCLUSIONS ...... 100

CHAPTER 6 ...... 102

6.1 ABSTRACT ...... 102 6.2 INTRODUCTION ...... 102 6.3 METHODS ...... 104 6.4 RESULTS ...... 109 6.5 DISCUSSION ...... 113

CHAPTER 7 ...... 116

7.1 INTRODUCTION ...... 116 7.2 CONCLUSIONS ...... 116 7.3 FURTHER WORK ...... 119

REFERENCES...... 122

APPENDIX A ...... 136

APPENDIX B ...... 153

APPENDIX C ...... 192

APPENDIX D ...... 258

APPENDIX E ...... ON CD

APPENDIX F...... ON CD

APPENDIX G...... ON CD

v List of Figures

FIGURE 1.1: THE DIVERSE RANGE OF BIRD SIZES AND HABITATS . TOP LEFT : OSTRICH (STRUTHIO

CAMELUS ) IN AN ISRAELI NATURE RESERVE (COURTESY OF JUDITH ANENBERG ). TOP RIGHT :

YELLOW WARBLER (DENDROICA PETECHIA ) FROM CANADA (COURTESY OF WIKIMEDIA

COMMONS ). BOTTOM LEFT : LAYSAN WITH CHICK (PHOEBASTRIA IMMUTABILIS ) FROM

MIDWAY ATOLL IN THE PACIFIC OCEAN (COURTESY OF RYAN HAGGERTY ). BOTTOM RIGHT :

LESSER BIRD OF PARADISE (PARADISAEA MINOR ) FROM NEW GUINEA (COURTESY OF RODERICK EINE )...... 1 FIGURE 1.2: EXAMPLE OF BAUM AND RAGAN CODING . AFTER SANDERSON ET AL . (1998)...... 4 FIGURE 1.3: COMPARISON OF SIBLEY AND AHLQUIST ’S “TAPESTRY ” (LEFT ) WITH THE SUPERTREE OF DAVIS (2003) (RIGHT )...... 11 FIGURE 1.4: FAMILY -LEVEL SUPERTREE FROM THE ANALYSIS CARRIED OUT BY DAVIS (2003). THIS REPRESENTS THE MOST COMPREHENSIVE KNOWN SUPERTREE OF AVES TO DATE ...... 14 FIGURE 2.1: MAP OF THE GREEN RIVER FORMATION . FROM BUCHHEIM AND EUGSTER (1998)...... 23 FIGURE 2.2. NEW SPECIMENS OF PRIMOBUCCO MCGREWI . TOP – SPECIMEN A, BOTTOM – SPECIMEN B. 26 FIGURE 2.3: BIOMETRIC GRAPHS SHOWING MEAN LIMB RATIOS FOR SPECIES OF PRIMOBUCCO . ALL MEASUREMENTS ARE IN MM AND ARE TAKEN FROM TABLE 2.1...... 29 FIGURE 2.4: STRICT CONSENSUS OF THE 18 MOST PARSIMONIOUS TREES RESULTING FROM ANALYSIS OF THE MATRIX IN APPENDIX E (LENGTH = 721, CI = 0.227, RI = 0.478, RC = 0.109)...... 31 FIGURE 2.5: ADAMS CONSENSUS OF THE 18 MOST PARSIMONIOUS TREES RESULTING FROM ANALYSIS OF THE MATRIX IN APPENDIX E (LENGTH = 721, CI = 0.227, RI = 0.478, RC = 0.109)...... 32 FIGURE 3.1: SUMMARY OF PROTOCOL FOR SELECTING SOURCE TREES . AFTER BININDA -EMONDS ET AL . (2004)...... 38 FIGURE 3.2: X AND Y ARE THE SAME SPECIES “Z”, WHICH RENDERS Z PARAPHYLETIC IN TREE (A). ONE

SOLUTION IS TO PRUNE EACH OF THE SOURCE SPECIES TO PRODUCE A SET OF SOURCE TREES

REFLECTING THE UNCERTAIN POSITION OF Z (B). IF TWO OR MORE SOURCE SPECIES OF Z FORM A

MONOPHYLETIC CLADE (W AND X IN TREE (A)), THIS CLADE CAN BE COLLAPSED TO A SINGLE TERMINAL (C). AFTER BININDA -EMONDS ET AL . (2004)...... 41 FIGURE 3.3: SCREENSHOT OF BIRD XML; A JAVA CLIENT FOR EASILY CREATING THE XML FILES ...... 44 FIGURE 3.4: GRAPHICAL REPRESENTATION OF MINIMAL OVERLAP OF SOURCE TREES (EXAMPLE FROM

CHAPTER 5). EACH NODE REPRESENTS A SOURCE TREE AND EDGES REPRESENT AN OVERLAP OF AT

LEAST TWO TAXA BETWEEN THOSE NODES . THE ISLAND CONSISTING OF FOUR SOURCE TREES 6, 7, 8 AND 19 SHOULD BE REMOVED FROM THE STUDY ...... 54 FIGURE 3.5: COMBINED SUPERTREE – SHOWN IS THE 50% MAJORITY -RULE CONSENSUS OF 8 MPT S OF LENGTH 961, FOUND IN TNT (G OLOBOFF ET AL ., 2008)...... 58 FIGURE 3.6: WEIGHTED SUPERTREE - SHOWN IS THE 50% MAJORITY -RULE CONSENSUS OF 17 MPT S OF LENGTH 11912, FOUND IN TNT (G OLOBOFF ET AL ., 2008)...... 59 FIGURE 3.7: HISTOGRAMS OF FIT SCORES FOR BOTH COMBINED AND WEIGHTED METHODS . NOTE THAT

NEITHER METHOD PRODUCES A GAUSSIAN DISTRIBUTION (WHICH IS DESIRABLE AS THE OPTIMUM

vi FIT WOULD BE ALL TREES WITH A SCORE OF 1 AND HENCE GIVE A NON-GAUSSIAN DISTRIBUTION )...... 60 FIGURE 3.8: BOX AND WHISKER PLOTS FOR COMBINED AND WEIGHTED DATA (SEE TABLE 3.1)...... 61 FIGURE 4.1: SINGLE MPT OF LENGTH 17899 FOUND BY TNT (G OLOBOFF ET AL ., 2008). THE INNER

RING SHOWS ORDERS , WHILST THE OUTER RINGS SPLIT THE PASSERIFORMES INTO MORE

MANAGEABLE SECTIONS (FAMILIES AND SOME GENERA ) TO BETTER SHOW AREAS OF INTEREST .

INDIVIDUAL TAXA ARE NOT VISIBLE , SEE APPENDIX C FOR A VERSION OF THE TREE IN WHICH ALL TAXA CAN BE READ ...... 71 FIGURE 5.1: DATA AVAILABILITY MATRIX FOR GREEN PLANT PROTEINS FROM GEN BANK (RELEASE

132). THE FIGURE SHOWS THAT THERE ARE A LARGE NUMBER OF GENES SAMPLED FOR ONLY A

FEW TAXA AND MANY TAXA SAMPLED FOR JUST A FEW GENES. EACH DOT REPRESENTS A SINGLE

GENE SAMPLED FOR A SINGLE TAXON . SPECIES WERE ORDERED ACCORDING TO THE NUMBER OF

GENES SAMPLED , WITH BETTER SAMPLED SPECIES AT THE TOP . SIMILARLY , THE MORE

COMMONLY USED GENES ARE TO THE RIGHT , SO THE TOP RIGHT CORNER CONTAINS THE DENSEST

CONCENTRATION OF DATA. THE REST OF THE MATRIX IS SPARSELY COVERED. FROM SANDERSON AND DRISKELL (2003)...... 85 FIGURE 5.2: GRAPHICAL REPRESENTATION OF MINIMAL OVERLAP OF SOURCE TREES AFTER PRUNING OF

NON -MOLECULAR SOURCE TREES . THE ISLAND CONSISTING OF FOUR SOURCE TREES NEEDS TO BE REMOVED FROM THE STUDY ...... 89 FIGURE 5.3: GRAPHICAL REPRESENTATION OF MINIMUM OVERLAP AFTER PRUNING OF THE FOUR DISCONNECTED TREES IN FIGURE 5.2...... 89 FIGURE 5.4: GALLIFORMES MOLECULAR SUPERTREE – SHOWN IS THE 50% MAJORITY -RULE CONSENSUS OF 12 MPT S OF LENGTH 426 FOUND IN TNT (G OLOBOFF ET AL ., 2008)...... 93 FIGURE 5.5: GALLIFORMES TREE FROM THE SUPERMATRIX ANALYSIS - SHOWN IS THE 50% MAJORITY -

RULE CONSENSUS OF 20400 MPT S OF LENGTH 41225 FOUND IN PAUP* 4.0 B10 (S WOFFORD , 2002)...... 94 FIGURE 5.6: GRAPH OF GENE COVERAGE FOR THE GALLIFORMES SUPERMATRIX . RED CIRCLES INDICATE CHARACTERS SAMPLED FOR EACH TAXON , THE SHADED BOX SHOWS MISSING DATA ...... 95 FIGURE 5.7: TANGLEGRAM SHOWING SIMILARITIES AND DIFFERENCES BETWEEN THE GALLIFORMES

SUPERTREE AND SUPERMATRIX . LINES ARE DRAWN BETWEEN CORRESPONDING TAXA ON EACH

TREE THEREFORE THE LESS LINES THAT ARE CROSSED INDICATES HIGHER SIMILARITY BETWEEN

THE TREES . COLOURS INDICATE FAMILIES /SUBFAMILIES AND ARE CODED AS IN FIGURES 5.4, 5.5 AND 5.6 ...... 96 FIGURE 5.8: BOX AND WHISKER PLOTS FOR THE SUPERTREE AND SUPERMATRIX (SEE TABLE 1 FOR INDIVIDUAL FIGURES )...... 98 FIGURE 6.1: THE YEAR OF PUBLICATION OF SOURCE TREES SHOWS A STRONG SKEW AMONG INCLUDED

TREES TOWARDS MORE RECENT ANALYSES . THE THREE MAJOR PEAKS (1990, 1999, 2004)

CORRESPOND TO THE PUBLICATION OF THE DINOSAURIA FIRST EDITION (W EISHAMPEL ET AL .,

1990), A SCIENCE REVIEW PAPER (S ERENO , 1999) AND THE DINOSAURIA SECOND EDITION (W EISHAMPEL ET AL ., 2004) RESPECTIVELY ...... 105

vii FIGURE 6.2: STANDARD MRP TREE WITH CLADE LABELS . MAJORITY -RULE WITH MINORITY

COMPONENTS CONSENSUS TREE OF THE REDUCED STANDARD MRP MATRIX SHOWING THE MAJOR

CLADES . ABBREVIATED CLADE NAMES ARE : MAM . = MAMENCHISAURIDAE , BR. =

BRACHIOSAURIDAE , HER . = HERRERASAURIDAE , COMPSOG . = "C OMPSOGNATHOIDEA ",

ORNITHOMIMO . = ORNITHOMIMOSAURIA , THERIZINO . = THERIZINOSAUROIDEA , ALVAR . = ALVAREZSAURIDAE AND , TROODON . = TROODONTIDAE ...... 107 FIGURE 6.3: RESULTS OF DIFFERENT ANALYSES OF DINOSAUR DIVERSIFICATION . A ) A SUMMARY

VERSION OF THE SUPERTREE USED HERE (F IGURE 6.2 FOR FULL TREE ); THE ELEVEN

STATISTICALLY SIGNIFICANT DIVERSIFICATION SHIFTS PRESENT IN BOTH THE ENTIRE TREE AND

AT LEAST ONE TIME -SLICE ARE MARKED WITH WHITE ARROWS DENOTING THE BRANCH LEADING

TO THE MORE SPECIOSE CLADE . TAXA IN BOLD REPRESENT THE COLLAPSING OF A LARGER CLADE ,

THE SIZE OF WHICH IS INDICATED IN PARENTHESES . AN ‘*’ INDICATES THE COLLAPSING OF A † PARAPHYLETIC CLADE AND A ‘ ’ AN EXTANT CLADE (I.E. BIRDS ). B ) DIVERSIFICATION RATES

BASED ON THE RAW RECORD (BLUE ), THE RAW RECORD PLUS ADDITIONAL ‘GHOST ’ RANGES

(GREEN ) AND SUBSAMPLED DATA (RED ; SEE TEXT ). C ) MEAN VALUES OF ∆2 SHIFT STATISTIC THROUGH TIME (SEE TEXT )...... 110

viii List of Tables

TABLE 1.1: SUMMARY OF FORMAL SUPERTREE METHODS ACCORDING TO CATEGORY . AFTER BININDA - EMONDS (2004)...... 6 TABLE 2.1: COMPARISON OF LIMB DIMENSIONS OF NEW SPECIMENS FMNH PA 611 AND FMNH 345 A /B TO OTHER SPECIMENS OF PRIMOBUCCO . ALL MEASUREMENTS ARE IN MILLIMETRES ...... 25 TABLE 3.1: STATISTICAL DATA FOR “FIT ” SCORES FOR BOTH COMBINED AND WEIGHTED METHODS .....61 TABLE 3.2: STATISTICAL DATA FOR “FIT ” SCORES FOR BOTH COMBINED AND WEIGHTED METHODS .....62 TABLE 5.1: STATISTICAL DATA FOR “FIT ” SCORES FOR BOTH THE SUPERTREE AND SUPERMATRIX ...... 98 TABLE 5.2: RUN TIMES FOR COMPUTATION OF BOTH TREES IN TWO DIFFERENT PROGRAMS ...... 99

ix CHAPTER 1: INTRODUCTION KATIE DAVIS

Chapter 1

Introduction

1.1 Introduction

Birds (Aves) are a diverse class and are the most abundant land vertebrates on the planet. There are approximately 10,000 species of extant birds (Monroe and Sibley, 1993) occupying almost every geographical location, from ocean to desert, and from woodland to lake (Figure 1.1). Birds are widely considered to have evolved from therapod dinosaurs during the period (Chiappe, 1995 and references therein), with the first known bird being the 150 million year old lithographica .

Figure 1.1: The diverse range of bird sizes and habitats. Top left: Ostrich (Struthio camelus ) in an Israeli nature reserve (courtesy of Judith Anenberg). Top right: Yellow Warbler ( Dendroica petechia ) from Canada (courtesy of Wikimedia Commons). Bottom left: with chick ( Phoebastria immutabilis ) from Midway Atoll in the Pacific Ocean (courtesy of Ryan Haggerty). Bottom right: Lesser Bird of Paradise (Paradisaea minor ) from New Guinea (courtesy of Roderick Eine).

1 CHAPTER 1: INTRODUCTION KATIE DAVIS

Birds are an economically important group, providing food for humans, as well as fertilizer, and some species are kept as pets. However, human activity may be partly to blame for the 1,107 species currently on the endangered species list (IUCN Red List, 2007). Phylogenies are an important tool in conservation, as highlighted by Nee and May (1997), and allow testing of hypothetical models to assess the loss of “phylogenetic diversity” (Bininda-Emonds et al., 2002). Birds are also in particular need of phylogenetic assessment as no widely accepted phylogeny currently exists. In fact, no complete phylogeny of Aves has been attempted since Sibley and Ahlquist’s “tapestry” (1990) was constructed using the much criticised technique of DNA-hybridisation. This phylogeny still only contained 1083 taxa, with most at -level. Smaller-scale attempts have also been made; the most recent of these being the large anatomical matrix of Livezey and Zusi (2007), which comprised just 150 taxa.

Phylogenies can be used for a range of practical applications in addition to aiding conservation, such as comparative biology and divergence times. A number of comparative studies using birds have been based on the tapestry of Sibley and Ahlquist (1990); these include the tempo and mode of bird (Nee et al., 1992), the effect of generation time on rates of avian molecular evolution (Mooers and Harvey, 1994) the evolution of avian mating systems and the association between mating systems and pair-bond length (Temrin and Sillen-Tullberg, 1994). The dependence of these comparative analyses on the tapestry is troubling as there are concerns about the validity of the method used (DNA – hybridisation) (Houde, 1987; Harshman, 1994; Sheldon and Bledsoe, 1993).

Given the lack of a comprehensive phylogeny of birds it is timely to create such a phylogeny. In order to include as many taxa as possible, a method must be used that allows the phylogeny to be as inclusive as possible. Supertree methods can be used to combine a large number of smaller individual phylogenies, each of which can be constructed using any phylogenetic techniques and any number of taxa, additionally these taxa may differ between these individual phylogenies. As such they give the widest possible view of phylogeny, both in terms of taxonomic coverage and in terms of the types of data incorporated.

2 CHAPTER 1: INTRODUCTION KATIE DAVIS

Large-scale supertrees have now been produced for many groups of taxa including the Dinosauria (Pisani et al., 2002; Lloyd et al. Chapter 6 of this thesis), marsupials (Cardillo et al., 2004), bats (Jones et al., 2002), early tetrapods (Ruta et al. 2003), grasses (Salamin et al. 2002), and a supertree of nearly all extant Mammalia (Bininda-Emonds et al., 2007). Avian supertrees have been produced for the (tube-nose ) (Kennedy and Page, 2002) and the (shorebirds) (Thomas et al., 2004) but not for all of Aves. Supertrees have been used to look at cladogenesis of primates (Purvis, 1995) and diversification of the Dinosauria (Lloyd et al., Chapter 6), amongst other things.

The purpose of this thesis is to construct a robust, and inclusive, phylogeny of Aves using supertree methods. As mentioned above, birds are a large important group of organisms, with nearly 10% of taxa currently on the endangered species list. Creating an inclusive phylogeny of birds will help elucidate their origins and help conservationists concentrate their efforts in preserving “biodiversity hotspots”.

1.2 Constructing large-scale phylogenies

There are two approaches used for creating large phylogenies. One is the supermatrix or “total evidence” method (Miyamoto, 1985; Kluge, 1989; Nixon and Carpenter, 1996). Here, all characters and taxa make up a single large matrix. A major drawback of this approach is that some types of data cannot be combined (e.g. immunological distance data and DNA-hybridisation data) and that combination of these data types introduces subjective decisions and is vastly time consuming (Sanderson et al., 1998). There is also the potential for a large amount of missing data when combining information in this way (Sanderson et al., 1998). Bird systematists have employed hard and soft body morphology, behaviour, allozymes, nucleotide sequences, and DNA-hybridisation to elucidate avian phylogeny. Consequently, a supermatrix approach would a priori eliminate many of these data sources.

However, supermatrices are based on primary character data and are thought to be capable of producing novel clades as a result of hidden character support with a well- characterised basis (Barrett et al., 1991; Gatesy et al., 1999; Lee and Huggal, 2003). When also taking into consideration the many issues with supertree construction,

3 CHAPTER 1: INTRODUCTION KATIE DAVIS some workers believe that supermatrices are far superior to supertree methods of constructing large phylogenetic trees (Gatesy et al., 2002; Gatesy et al., 2004; Queiroz and Gatesy, 2006).

The second approach is the supertree method. A supertree is defined as an estimate of phylogeny assembled from smaller phylogenies. These partial phylogenies must have some taxa in common, but not necessarily all (Sanderson et al., 1998). Supertrees are constructed, not from primary data, but from the combining of the topologies of partial phylogenies into a single comprehensive matrix (Bininda- Emonds et al., 1999). Trees contributing to a supertree analysis are known as “source trees”. The most commonly used supertree method is Matrix Representation with Parsimony (MRP) (Baum and Ragan, 2004). All taxa subtended by a given node in a source tree are scored as “1”, taxa not subtended from that node are scored as “0”, taxa not present in that source tree are scored as “?”. Trees are rooted with a hypothetical, all-zero outgroup (Ragan, 1992) (Figure 1.2).

Figure 1.2: Example of Baum and Ragan coding. After Sanderson et al. (1998).

One of the justifications for the use of supertree methods is that they can combine trees derived from all data types to produce a single phylogeny (Sanderson et al., 1998). However, the main advantages of supertrees are that they can handle very large numbers of taxa, combine numerous types of characters in a single tree,

4 CHAPTER 1: INTRODUCTION KATIE DAVIS potentially summarise support, resolve groups that are poorly resolved in source trees, resolve taxon conflict (Ruta et al., 2003) and highlight poor taxonomic sampling (Salamin et al., 2002). However, it is not universally agreed that supertrees are a robust method for constructing phylogenies and criticisms include the use of poorly justified source data (Gatesy et al., 2002) and biases in supertree methods (Wilkinson et al., 2005b).

Some of these criticisms will be addressed in this thesis with the production of a rigorous supertree-building protocol, and in addition, supertree and supermatrix methods will be compared and contrasted using a case study. Supertree methods will also be used to construct species-level phylogenies for all Aves and Dinosauria. As discussed above, supertree methods are likely to be more efficient and will enable the incorporation of a wider variety of data, increasing taxonomic coverage. There are numerous different methods currently available for creating supertrees, not all of which have software implementation. These are discussed in more detail below.

1.3 Supertree methods

There are several implementations of the supertree approach. Of these the only widely used method is Matrix Representation with Parsimony (MRP). Methods can be split into two broad categories; “agreement” and “optimisation”. Agreement methods find common or uncontested groups within a set of source trees. In contrast, optimisation methods find the supertree (or set of supertrees) that has the maximum fit to the set of source trees according to an objective function (Bininda-Emonds, 2002). A summary table of all current supertree methods can be found in Table 1.1.

The main methods to date that have software implementation are Matrix Representation with Parsimony (MRP), Matrix Representation with Flipping (MRF), Matrix Representation with Compatibility (MRC), Mincut (MC) and Modified Mincut (MMC). These are all discussed in more detail in the section below.

5 CHAPTER 1: INTRODUCTION KATIE DAVIS

Table 1.1: Summary of formal supertree methods according to category. After Bininda-Emonds (2004).

Agreement Supertrees Optimisation Supertrees MinCutSupertree Average consensus (MRD) Modified MinCut Bayesian supertrees RankedTree Gene tree parsimony Semi-labelled and AncestralBuild Matrix representation using compatibility (MRC) Semi-strict Matrix representation using flipping (MRF or MinFlip) Strict Matrix representation with parsimony (MRP) and variants Strict consensus merger Most similar supertree method (dfit) Quartet supertree

1.3.1 Matrix Representation with Parsimony (MRP)

Matrix Representation with Parsimony (MRP) is by far the most widely used method and has been used to construct most large supertrees to date, for organisms ranging from dinosaurs (Pisani et al., 2002) to flowering plants (Linder, 2000). This method can be used whether or not source trees are compatible, and converts the topology of a source tree into a data matrix of “characters” (Sanderson et al., 1998). Once an MRP matrix has been constructed it can be analysed using a number of different computational algorithms. For example, the dinosaur supertrees (Pisani et al., 2002; Lloyd et al., Chapter 6 this thesis), mammals (Bininda-Emonds et al., 1999; Cardillo et al., 2004) and supertrees (Kennedy and Page, 2002) have all been constructed using MRP. Matrix Representation with Parsimony methods seek to find a tree that requires the fewest number of steps based on the input matrices.

MRP is not however without criticisms. Gatesy et al. (2004) claim that although the majority of published supertree analyses have been constructed using MRP (e.g. Purvis, 1995; Bininda-Emonds et al., 1999; Daubin et al., 2001; Liu et al., 2001; Jones et al., 2002; Kennedy and Page, 2002; Salamin et al., 2002) the logical basis, they claim, for this is unclear. They state that “using MRP to summarise the results of different analyses amounts to finding the arrangement of taxa that provides the best explanation of the conclusions of those analyses, not the best explanation of observations.”.

6 CHAPTER 1: INTRODUCTION KATIE DAVIS

Gatesy et al. (2002) also state that constructing supertrees is not the same as constructing cladograms from primary data and should not be interpreted as such as they are based on secondary representations of data. Bryant (2004), however, suggests that MRP could be operationally equivalent to the construction of cladograms using cladistic analysis of character data if consistent with cladistic principles and the following properties are upheld:

1) Must be based on source trees that were generated using well-designed cladistic analyses.

2) Matrix elements or sets of matrix elements should be weighted based on the relative character support for individual nodes on the source trees and to alleviate inappropriate biases associated with tree size.

3) Source trees should have high consistency indices.

4) The source trees must be based on different sets of characters to guarantee independence among the matrix elements.

Bryant (2004) concluded that all published MRP analyses failed to meet these criteria and therefore should be considered a synthesis of information rather than a rigorous phylogenetic analysis.

However, an advantage of Matrix Representation with Parsimony is that it has numerous software implementations including PAUP* 4.0b10 (Swofford, 2002) TNT (Goloboff et al., 2008), POY (Varón et al., 2007) and Clann (Creevey and McInerney, 2005).

1.3.2 Matrix Representation with Flipping (MRF)

Minimum flip (MRF) supertrees attempt to find the minimum number of changes (“flips”) to the matrix of source trees that will resolve incompatibilities (Eulenstein et al., 2004). A cell in the matrix representation has either a 1 or a 0 and can be regarded as a potential error (Burleigh et al., 2004). MRF determines the minimum number of flips required to turn this matrix into one that corresponds to a tree with no homoplasy (MRP seeks to find the tree with the least homoplasy). If the source

7 CHAPTER 1: INTRODUCTION KATIE DAVIS trees are compatible and no flips are necessary the resulting supertree will display all the input trees.

MRF represents a philosophically different approach to that taken by MRP methods as it is based on error correction in the source trees, whereas MRP seeks to find the supertree with the minimum number of character changes with respect to the matrix representation (Eulenstein et al., 2004).

Eulenstein et al. (2004) found that their MRF heuristic was at least as accurate as MRP methods and more accurate than MC or MMC supertrees. Accuracy was assessed by the use of MAST and triplet scores comparing the supertrees to the source data. Simulations showed that for calculating large phylogenies from a large collection of small input trees MRF should perform more accurately than any of MRP, MC or MMC supertrees. The major drawback of this method is the speed of the algorithm. In terms of speed, MRF was outperformed by MC (MinCut), MMC (Modified MinCut) and MRP (Matrix Representation with Parsimony) algorithms and it was only feasible to compute a 96 taxon supertree with the MRF algorithm. Obviously this becomes problematic when attempting to reconstruct phylogenies of groups containing, not just 100s, but 1000s of taxa.

1.3.3 Matrix Representation with Compatibility

Matrix Representation with Compatibility (MRC) identifies the largest set of mutually compatible characters in combined datasets represented by a binary matrix (Ross and Rodrigo, 2004). Compatible characters are those that either support, or are consistent with, a particular phylogenetic tree. These sets of characters are known as cliques and MRC seeks to find the largest set of these characters, known as the “maximum clique” (Ross and Rodrigo, 2004).

Overall, MRC does not perform as well as MRP. Both are successful but MRP is slightly more so for “large” datasets of 7-10 trees in which >50% taxa overlap is present (Ross and Rodrigo, 2004), although this clearly is not large in the context of most supertree analyses and certainly not in terms of this thesis. Ross and Rodrigo (2004) consider the main benefit of MRC to be that it “identifies the consistent and uncontradicted core of the dataset and excludes those nodes which logically cannot

8 CHAPTER 1: INTRODUCTION KATIE DAVIS exist”. Its main failing however is that it is not practical for the construction of large supertrees as it takes such a long time to find the maximum cliques in large datasets (Ross and Rodrigo, 2004).

1.3.4 MinCut

MinCut is derived from the OneTree algorithm (Ng and Wormald, 1996), which is a recursive algorithm that only returns a tree if all the input trees are compatible. MinCut (Semple and Steele, 2000) modifies OneTree such that it always returns a tree even if input trees are incompatible. MinCut contains slightly disconcerting properties when using simple test cases, for example, producing polytomies for uncontradicted data and maintaining relationships for contradicted data (Page, 2002). The algorithm uses a connective graph whose edges have a weight associated with them, this weight is the number of input trees that contain that relationship. Any edges that have the same weight as the number of input trees (i.e. unanimous/uncontradicted) are removed by merging the nodes. All edges that do not have the same weight as the number of source trees (i.e. contradicted) are placed in a polytomy. From this modified graph a new tree can be constructed.

1.3.5 Modified MinCut

Modified MinCut (Page, 2002) is based directly on MinCut but modifies the definition of “unanimous and uncontradicted”. “Unanimous” means the same as in MinCut (Semple and Steele, 2000), however “uncontradicted” is defined as a nesting found in some of the source trees that is not contradicted by any of the source trees. This results in the collapsing of more nodes and removes the spurious groupings that can be returned by MinCut. Simulation studies (Eulenstein et al., 2004) show that MinCut and Modified MinCut do not work as well as other methods, so it is reasonable to dismiss these a priori as potential supertree-building mechanisms for this study.

1.3.6 Other methods

A number of other methods exist in theory but have no software implementation as yet. A few of note are mentioned below.

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Daniel and Semple (2004) described a supertree algorithm for higher taxa. This assumes that all operational taxonomic units (OTUs) are species and thus labels interior nodes as higher taxa, therefore trees with higher taxa can be included with no need for any processing. Also, the problem can be solved in polynomial time. A potential problem though is that it assumes that the is correct.

Semi-strict supertrees (Goloboff and Pol, 2002) find a subset of the whole matrix where all possible subsets are compatible; this is known as the “ultra-clique”. Finding this ultra-clique is computationally complex but a heuristic method provides good results. If trees have no conflict or there are only two source trees then this method will get an exact result. When there are more than two and there is conflict, it eliminates spurious groups to find supertree. The drawback is that supertrees from matrices with very dissimilar sets of taxa (with not much overlap) should be interpreted with caution as they produce unresolved semi-strict supertrees.

1.4 Current estimates of Avian Phylogeny

1.4.1 The Sibley and Ahlquist tapestry

Current views on avian phylogeny are largely derived from Sibley and Ahlquist’s “tapestry” (1990). Many comparative studies have also been carried out using this work (Mooers and Harvey, 1994; Temrin and Sillen-Tullberg, 1994). The “tapestry” consisted of DNA work carried out by Sibley and Ahlquist over many years culminating in the publication of the book “Phylogeny and classification of birds – A study in molecular evolution” (1990). It covered 1083 taxa, most at genus level, and is the most comprehensive published study of avian phylogeny to date (Figure 1.3).

The DNA-hybridisation technique measures the genetic distance between taxa and Sibley and Ahlquist (1990) state that “a phylogeny based on DNA distances is a diagram of the degrees of genetic divergence among the included taxa”. The major criticisms of this technique are the fact that the authors did not publish the raw data (Houde, 1987), and that it was based on incomplete distance matrices and used an inappropriate tree-building algorithm (Harshman, 1994). Houde (1987) also points out that the avian molecular clock was assumed to be constant, but this is not the case in reality. The final point is that the method is phenetic, not cladistic, using

10 CHAPTER 1: INTRODUCTION KATIE DAVIS distances instead of characters (Sheldon and Bledsoe, 1993). Some authors have, however, confirmed some of Sibley and Ahlquist’s results (Harshman, 1994; Bleiweiss et al., 1994).

In addition, Sibley and Ahlquist’s tapestry was constructed largely at genus level and only covered 1083 taxa (including some higher taxa and vernacular names) out of an estimated 10,000 known species of birds (Monroe and Sibley, 1990). Therefore, it is clear that it is time for a new estimate of avian phylogeny, and supertree methods are an ideal way of exploring this in much greater detail than achieved previously.

Figure 1.3: Comparison of Sibley and Ahlquist’s “tapestry” (left) with the supertree of Davis (2003) (right).

1.4.2 Family-level supertree

To summarise knowledge of large-scale avian phylogeny prior to this thesis, the family-level supertree constructed as part of the author’s M.Sc thesis will be used (Davis, 2003). In this study 124 source trees and 199 taxa were included. This supertree includes both extinct and extant taxa starting with the first known bird, the Jurassic Archaeopteryx lithographica . This supertree was a preliminary study of large-scale avian phylogeny and will be used in this thesis in lieu of a literature review in order to summarise current knowledge of avian phylogeny. The supertree provides a useful tool for this purpose and shows the current “state of the art”.

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Overview of avian phylogeny from the family-level supertree

The family-level supertree also included the use of QS values (Bininda-Emonds, 2003) to investigate clade support. This is described first below before discussing the supertree in depth.

The average QS value for the supertree was –0.043. Qualitative Support (QS index), is one of the first support measures that samples at the level of source trees rather than characters (Bininda-Emonds, 2003) and, as such, is possibly the first method that can be successfully applied to supertrees. The QS index works by comparing source trees with the supertree and assigning one of four “states” for the fit between the two. A hard match occurs where the source tree fits the supertree exactly, a soft match occurs where addition of missing taxa may support the clade but never contradict it and vice versa for a soft mismatch, finally, a hard mismatch occurs where the source tree contradicts the supertree. Hard matches are scored as +1, soft matches as +0.5, equivocal matches as 0, soft mismatches as –0.5 and hard mismatches as –1. These values are summed over the clade and divided by the number of source trees, therefore the QS value for a clade indicates the proportion of matches and mismatches in the clade. Generally speaking, more matches result in a positive QS value and more mismatches produce a negative value (Bininda-Emonds, 2003). Of 161 clades, none have hard support, which is to be expected as only highly overlapping datasets are likely to show hard support (Bininda-Emonds, 2003). Equally, no clades show hard conflict, indicating that there are no novel clades present in the supertree. Soft support was found in 37% of clades, while soft conflict was found in 58%. The remaining 5% were equivocal. The average clade size showing soft conflict was much larger than that for soft support (31.366 taxa as opposed to 9.250, respectively), this is due to the increasing possibility of disagreement between source trees as numbers of taxa increase (Bininda-Emonds, 2003). Equivocal clades have the highest average taxa number (179.375) and are all found near the base of the tree. This is in contrast to the results of Bininda-Emonds (2003), who found that equivocal clades largely follow the trends seen in clades with soft support. Overall, the tree is well resolved, with the exception of clades within the Passeriformes and a large part of the Ciconiiformes.

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The resultant supertree (Figure 1.4) was the 50% majority rule consensus of 1,387 MPTs and had a length of 1109 steps. Low QS values reflect uncertainty in the positions of Mesozoic taxa relative to one another. The Mesozoic taxa were also the least well-represented among the source trees occurring, on average, in just 9% of the source trees. Despite the well-supported position of Archaeopteryx at the base of the tree (QS value of 0.5), only two clades have relatively high support; the , which all have values higher than the tree average, and the Hesperornithiformes, which all have positive support values. This probably reflects the fact that the Enantiornithes and Hesperornithiformes are well studied groups, in contrast to other Mesozoic taxa many of which are represented by only a handful of and have been included in few phylogenetic analyses.

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Figure 1.4: Family-level supertree from the analysis carried out by Davis (2003). This represents the most comprehensive known supertree of Aves to date.

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Positions of extant orders are poorly understood, a fact that is reflected in the relatively low QS values for many clades. Palaeognath (ratites and ) monophyly is retained; this clade is well supported compared to many others when QS values are taken into account. This result is in contrast to the proposal that the are actually polyphyletic (Houde and Olson, 1981). The supertree also supports monophyly of the Galloanserae, a relatively recent proposal that the (waterfowl), Craciformes and Galliformes (landfowl) comprise a monophyletic group (Caspers et al., 1997; Van Tuinen et al., 2000; Sorenson et al., 2003). The position of the Galloanserae with respect to other orders has been debated, specifically whether they form a monophyletic clade with the Palaeognathae (Sibley and Ahlquist, 1990) or occupy the position of sister group to the (Neornithes minus ) (Cracraft, 1988; Van Tuinen et al., 2000).

The traditional classification of the ( and allies) originally encompassed the clade now known as the Galbuliformes () (Simpson and Cracraft, 1981; Swiersczewski and Raikow, 1981). Several authors have suggested that the traditional Piciformes were polyphyletic and that the Galbulae (the modern Galbuliformes) were more closely related to the Coraciiformes (kingfishers and allies) (Sibley and Ahlquist, 1972; Olson, 1983; Burton, 1984). The supertree places the Piciformes in a separate clade to the Coraciiformes and Galbuliformes, supporting the hypothesis that the latter two orders are more closely related to each other than either is to the Piciformes. These two clades are among the strongest in the tree, both with relatively high QS values compared to the tree average (0.012 and 0.016 respectively). Psittaciformes ( and allies) are traditionally considered to have no close living relatives (Sibley and Ahlquist, 1990) while the supertree suggests a sister group relationship with the Piciformes.

The closest relatives of the Columbiformes (doves and pigeons) are historically not well understood (Sibley and Ahlquist, 1990). This analysis suggests a sister group relationship with the (swifts) and Trochiliformes (), and with the Strigiformes (). This clade is also one of the stronger groupings within the tree with a QS value of -0.016. The association between Apodiformes and Trochiliformes is well recognised (Bleiweiss et al., 1994; Van Tuinen et al., 2000;

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Johansson et al., 2001; Mayr, 2002) and is not contradicted by any of the source trees. The positioning of Strigiformes as sister group to these taxa also agrees with that found by Bleiweiss et al. (1994).

Turniciformes (buttonquail), Cuculiformes ( and anis) and Ciconiiformes ( and allies) comprise another clade, in agreement with Van Tuinen et al. (2000). The affiliation between Turniciformes and Ciconiiformes is also recovered by the analysis of Groth and Barrowclough (1999). Sibley and Ahlquist (1990) greatly expanded the definition of the Ciconiiformes to subsume the traditional orders Charadriiformes (shorebirds), (diurnal birds of prey), Pelicaniformes (totipalmate birds, e.g. and ), Procellariiformes (tube-nose seabirds), Podicipediformes (), () and Sphenisciformes (). This is the most controversial part of Sibley and Ahlquist’s classification and many of these taxa are placed within a large polytomy reflecting the high degree of incongruence between the source trees. These basal nodes within the Ciconiiformes have low QS values compared to the tree average, also indicating low support and high degrees of source tree conflict. Taxa that are resolved include the traditional “Falconiformes”, a number of “pelicaniform” taxa and two clades of “procellariiform” taxa. All these groups retain monophyly according to the traditional classification of orders suggesting that their inclusion within this expanded Ciconiiformes may not be justified. In addition, they all possess positive QS values, indicating that their monophyletic status is largely uncontradicted. In addition to “falconiform” monophyly, the supertree confirms polyphyly of Old and New World vultures. Cathartidae (New World vultures) are closely related to Ciconiidae (storks), and Accipitridae (Old World vultures) are placed within the traditional Falconiformes. Three controversial taxa within the Ciconiiformes are the Spheniscidae (penguins), Gaviidae (loons) and Podicipedidae (grebes). These taxa have been placed in widely differing positions in previous analyses. They have been considered to be closely related (Cracraft, 1985) and some analyses (Sibley and Ahlquist, 1990) have claimed that loons and penguins are related to each other, and to Procellariiformes, while grebes have no close living relatives. A more recent analysis (Van Tuinen et al., 2001) showed that grebes may be related to . This issue is not resolved with the current analysis as,

16 CHAPTER 1: INTRODUCTION KATIE DAVIS although the Podicipedidae appear to be related to the Charadriidae, both the Gaviidae and Spheniscidae are part of the large polytomy.

The pairing of Musophagiformes () with Coliiformes (), and Trogoniformes () with the , is supported by Van Tuinen et al. (2000). In the supertree these taxa are placed as sister groups to the Passeriformes (perching birds). The Passeriformes are traditionally considered to be a monophyletic group that evolved more recently than most other avian lineages (Johansson et al., 2001). Some recent molecular analyses, however, have placed the at the base of the avian phylogenetic tree (Härlid et al., 1998; Mindell et al., 1999) and also as a paraphyletic group (Mindell et al., 1999), but this has since been rejected (Garcia-Moreno et al., 2003). This view is also not supported by the supertree analysis, which agrees with the traditional view that the Passeriformes diverged relatively late compared to many other orders. However, QS values for Passeriformes are, on average, lower than the tree average, indicating the presence of conflict within the source trees. Acanthisittidae (New Zealand wrens) are placed at the base of the Passeriformes. This is as suggested by many workers who have been unable to assign them to either the suboscines or the oscines (e.g. Lovette and Bermingham, 2000). All other passeriform taxa are split into the suboscines and oscines. The suboscines are divided into well supported (QS higher than tree average) Old and New World clades, the latter being further subdivided into tracheophone and non-tracheophone clades.

Menuridae (lyrebirds) occupy the basal-most position within the oscines as proposed by many workers (e.g. Ericson et al., 2002). The majority of the remaining oscines are grouped into three clades. Although QS values are low for these clades, the relationships fit very well the model proposed by Christidis and Schodde (1991) where the Australo-Papuan (Sibley and Ahlquist’s “”) are clustered into two main assemblages representing two endemic radiations. One includes the and allies (Meliphagidae, Acanthizidae and Orthhonychidae); the other contains the corvoid birds. These groups are analogous to Sibley and Ahlquist’s Meliphagoidea and Corvoidea. The remaining families comprise the Eurasian radiation (Sibley and Ahlquist’s “”). The supertree supports this model, although the “Corvida” are part of a polytomy and may or may

17 CHAPTER 1: INTRODUCTION KATIE DAVIS not prove to be monophyletic. The “Passerida”, however, form a distinct monophyletic clade, as also found by Christidis and Schodde (1991). This pattern of relationships has been used to suggest a Gondwanan origin for the Passeriformes (Ericson et al., 2002), although the supertree has been unable to resolve the three clades with respect to each other, and therefore, while not in opposition to this hypothesis, does not directly support it.

Within the Eurasian oscines, it is generally accepted that the nine-primaried oscines comprises two sister clades; one being the family Fringillidae and the other made up of the Emberizidae, Coerebidae, Parulidae and Icteridae (Klicka et al., 2000). The supertree shows that while the second clade forms a monophyletic group, the Fringillidae are more closely associated with the Passeridae and , as suggested by Groth (1998). Groth suggested that the term “New World nine- primaried oscines” might be best restricted to the emberizids (Emberizidae, Coerebidae, Parulidae and Icteridae) alone, as the traditional monophyletic grouping is not supported. The supertree suggests that this view may well be correct. In addition to this the fringillids are primarily an Old World group, which supports their separation from the New World nine-primaried oscines (Groth, 1998).

1.4.2.1 Limitations

The above section provides a good general overview of avian phylogeny, however, there are many areas for potential improvement. There was no attempt at standardising the taxonomy and, as a result, the tree will almost certainly contain synonyms that should be dealt with. The method used was cumbersome and error- prone as the data were processed largely by hand. There was a loss of important data, such as the method used in the original study, and finally, it would be much more useful to carry out meaningful comparisons on a supertree constructed at species- level. The support measures used (QS values) are also flawed as the categories defined by Bininda-Emonds (2003) were not mutually exclusive, for example the definitions of equivocal and soft support both contain no hard matches or mismatches and both contain soft mismatches (Wilkinson et al., 2005a). For this reason, QS values will not be utilised for the supertrees in this thesis.

18 CHAPTER 1: INTRODUCTION KATIE DAVIS

Issues surrounding data independence are also important in supertree construction. This study used 124 source trees and every effort was made to ensure the quality of the data used. However, ideas differ as to what constitutes an acceptable source tree and since this study was carried out, Bininda-Emonds et al. (2004) have proposed a protocol for selecting suitable source trees.

1.5 This thesis

There are clear issues that affect the family-level supertree (Davis, 2003) as outlined above. This thesis aims to construct species-level supertrees of all avian and dinosaurian taxa. The main challenges for this are data collection and processing; that is ensuring that data are faithfully recorded from the source and processed in a consistent and logical manner with minimal errors. The methodology used in the family-level supertree (Davis, 2003) is not suitable for such an endeavour as that study relied on manual data processing, which will not be possible for a significantly larger dataset. In addition, new ideas on how to minimise the problems associated with supertree construction have arisen since that study. It is therefore the aim of this study to implement and test these and see what effect they have on supertree construction. The questions posed in this thesis are:

1. Can a protocol for constructing supertrees be developed that is both methodologically robust and easy to implement?

2. Does this protocol result in supertrees that are good representations of the source data?

3. Can a supertree of all Aves be constructed at species-level using this protocol?

4. Can community-based tree-building help speed up the process in finding shorter tree?

5. Do supertree methods compare favourably with trees found from supermatrix analyses? Which, if either, produces superior results?

6. Can a new, updated supertree of the Dinosauria shed light on dinosaur diversification throughout the Cretaceous?

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1.6 Thesis summary

The next chapter looks into the input for supertree construction; the source tree. Here, new specimens of the taxon Primobucco mcgrewi are described and primary character diagnosis is encoded. The new information gleaned from these fossils is used to construct a phylogenetic tree, which can be used as input for a supertree. The results of this have not been included in the supertree in this thesis as it has not yet been published and this would violate the protocol designed and described in Chapter 3. This chapter has been written as a paper for submission to Neues Jahrbuch für Geologie und Paläontologie in collaboration with G. J. Dyke of University College Dublin.

Chapter 3 deals with the construction of supertrees. A protocol, based on that of Bininda-Emonds et al. (2004), is proposed and tested using a relatively small monophyletic group; the Galliformes (landfowl).

Once a suitable protocol is defined, and tested, the avian supertree is constructed and described in Chapter 4. This tree includes both extant and extinct species and is an order of magnitude greater in terms of taxa number than previous studies – a step- change in supertree size.

Given that the supertree method has been criticised, a small test, again involving the Galliformes, between supertree and supermatrix methods has been carried out in Chapter 5. The two methods were used on the same data, using identical numbers of taxa.

Dinosaurs are widely considered to be the ancestors of Aves (Chiappe, 1995 and references therein), and as such it is interesting to consider a supertree of Dinosauria. The first dinosaur supertree was published in 2002 (Pisani et al., 2002) and this chapter details an updated tree with the inclusion of additional new data and the use of a strict protocol, adapted for extinct taxa. The tree is then used to look at diversification of the Dinosauria and to test the hypothesis of a major “burst” in diversification during the Campanian and Maastrichtian (Fastovksy et al., 2004). This work was co-authored with G. T. Lloyd (University of Bristol), D. Pisani (National University of Ireland, Maynooth), J. Tarver (University of Bristol), M. Ruta (University of Bristol), M. Sakamoto (University of Bristol), D. W. E. Hone

20 CHAPTER 1: INTRODUCTION KATIE DAVIS

(Bayerischen Staatssammlung für Paläontologie und Geologie), R. Jennings (University of Bristol), and M. J. Benton (University of Bristol).

Finally, the thesis is concluded in Chapter 7, which brings together the previous chapters, provides answers to the questions posed above and offers suggestions for future work.

21 CHAPTER 2: PRIMOBUCCO KATIE DAVIS

Chapter 2

Two new specimens of Primobucco (Aves: Coraciiformes) from the Eocene of North America

2.1 Abstract

The Primobucconidae are fossil birds known from the Eocene of North America and Europe. This paper describes two new partial specimens from the Green River Formation of Wyoming (USA). Both specimens were assigned to the species Primobucco mcgrewi . Although incomplete, these specimens have preserved anatomical features not seen in other material and therefore add to our knowledge of these extinct birds. The two specimens were added to the large morphological matrix of Mayr and Clarke (2004) in an attempt to further constrain their phylogenetic position. The results of the analysis were inconclusive, showing only that the Primobucconidae appear to belong in a clade containing the extant Coraciiformes and related taxa. The new characters provided by these new specimens do, however, provide a wealth of new information and will surely prove invaluable in future analyses of these fossil birds.

2.2 Introduction

The Primobucconidae comprise a clade of fossil birds thought to be related to extant rollers (Mayr et al ., 2003), Coraciiformes. They are known from the Eocene of North America and Europe – fossil material has been described from the Lower Eocene Green River Formation of North America (Brodkorb, 1970; Houde and Olson, 1989; Mayr et al., 2004), the Lower Eocene of France (Mayr et al., 2004), and the Lower-Middle Eocene of Messel, Germany (Mayr et al., 2004). However, in spite of recent discoveries, including some complete but crushed skeletons (Mayr et al., 2004), their systematic position still remains somewhat uncertain (Mayr et al., 2004).

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The earliest described specimen of Primobucconidae, the of Primobucco mcgrewi , was discovered in the Green River Formation (Brodkorb, 1970) and described based on an incomplete right wing. More recently, new specimens have been allocated to Primobucco , including two new species; P. perneri and P. frugiligeus (Mayr et al., 2004). These specimens were incorporated into a cladistic analysis of morphological characters by Mayr et al. (2004) who considered Primobucconidae to occupy an unresolved basal position within Coraciiformes (sensu Mayr, 1998; see Mayr et al., 2004: figure 6).

In this paper, we augment the known composition of Primobucconidae by describing two new specimens of Primobucco mcgrewi also from the Green River Formation of Wyoming (USA) (Figure 2.1). These specimens, although incomplete, add new anatomical features not seen in previously described material.

Abbreviation: FMNH, Field Museum, Chicago.

Figure 2.1: Map of the Green River Formation. From Buchheim and Eugster (1998).

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2.3 Systematic palaeontology

Anatomical terminology used here follows Howard (1980) and Baumel (1979).

Order Coraciiformes sensu stricto (see Mayr, 1998)

Family Primobucconidae Feduccia and Martin, 1976

Genus Primobucco Brodkorb, 1970

Species of Primobucco are all similar in their morphology and have been distinguished from one another based on differences in their limb proportions and overall size (Mayr et al., 2004). Because of the compressed nature of many specimens, other osteological features have yet to be identified. These new specimens are therefore assigned to P. mcgrewi on the basis of limb measurements and ratios (see Table 2.1 for measurements and Figure 2.3) and inferences from modern rollers.

Primobucco mcgrewi Brodkorb, 1970

2.3.1 Original material

The holotype, UWGM 3299, consists of a right wing (Brodkorb, 1970).

2.3.2 Referred specimens

FMNH PA 611, slab containing right and left forelimbs, sternum and shoulder girdle (Figure 2.2 – top). The right wing is almost complete comprising the humerus, radius, ulna, carpometacarpus, phalanx digiti majoris and phalanx digiti minoris. The left wing is less complete; the humerus, radius, ulna, proximal end of the carpometacarpus and the phalanx digiti alulare are present. The sternum and incomplete disarticulated shoulder girdle are present consisting of both coracoids and a partial scapula. FMNH PA 345 a/b (part and counterpart), slab containing well- preserved forelimbs, sternum and shoulder girdle (Figure 2.2 – bottom). In this specimen, the right wing comprises the humerus, radius, ulna and the proximal carpometacarpus and the left comprises the proximal humerus and distal radius and ulna. The sternum is present with five costal processes preserved on its right side. The incomplete shoulder girdle includes the left and right coracoids.

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2.3.3 Dimensions

Table 2.1: Comparison of limb dimensions of new specimens FMNH PA 611 and FMNH 345 a/b to other specimens of Primobucco. All measurements are in millimetres.

Humerus (R/L) Ulna (R/L) Carpometacarpus (R/L) Primobucco mcgrewi Brodkorb, 1970 Holotype (after 26.7/- ~34.2/- ~14.2/- Brodkorb, 1970) USNM 336284 (after ~27/~28 ~32.5/~33 -/15.3 Mayr et al. , 2004) UWGM 14563 (after -/26.8 -/33.8 -/15.7 Mayr et al. , 2004) FMNH PA 611 30.8/29.7 39.6/39.6 17.6/- FMNH PA 345 a/b 27.5/- 35.2/- -/- Primobucco perneri Mayr et al. 2004 Holotype (after Mayr et ~29.3/~29.3 ~36.3/36.0 15.4/15.1 al. , 2004) SMF-ME 3793 (after -/~25.8 - -/~15.0 Mayr et al. , 2004) SMF-ME 516 (after ~25.2/~26.5 -/~32.0 15.0/15.0 Mayr et al. , 2004) SMF-ME 3546 (after ~28.6/~28.9 -/~34.0 -/~17.1 Mayr et al. , 2004) Primobucco frugilegus Mayr et al. 2004 Holotype (after Mayr et ~31.5/- ~37.8/- 18.7/- al. , 2004) SMF-ME 3794 (after ~32.7/~32.7 -/~38.4 ~19.4/- Mayr et al. , 2004)

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2.3.4 Collection history

Both FMNH PA 611 and FMNH PA 345 were collected from the Fossil Butte Member of the Green River Formation, Lincoln County, Wyoming (USA). FMNH PA 611 was collected by T. Lindgren and the Green River Geological Labs in 1990 while FMNH PA 345 was collected by J. E. Tynsky in 1983.

Figure 2.2. New specimens of Primobucco mcgrewi . Top – specimen A, bottom – specimen B.

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2.3.5 Description

The Primobucconidae are small birds and both the specimens reported here have a wingspan of approximately 21 cm (see Table 2.1 for dimensions of individual elements).

The coracoid is long and thin with a broad distal end. The processus procoracoideus is short, but not abbreviate – it projects as far as the acrocoracoideus. The extremitas omalis is elongate and the processus lateralis of the extremitas sternalis is narrow. There is no notch on the medial margin of the sternal end. The processus lateralis is hooked cranially and the facies articularis sternalis located primarily on the dorsal surface.

The scapula is long and blade-like; the distal end is not preserved. The acromion is not bifurcate and has no distinct medial process. The extremitas caudalis is markedly hooked and deflected away from the plane of the bone.

The sternum is short and broad; being slightly longer than it is wide, there are four deep notches in the caudal end. Both pairs of incisions are very deep; the lateral ones are deeper than the medial ones, reaching to approximately half the length of the corpus sterni. The processus craniolaterales are long and prominent. The sternal keel is long and extends for most of the length of the corpus sterni. The spina externa is present and well-developed.

The humerus is elongate and slightly curved, its head is large, inflected medially and is short and broad. The distal border of the head merges into the shaft indistinctly; the entire caput humeri is medial to the inner border of the shaft. A small tuberculum dorsale is present and the crista deltopectoralis is short and protruding. The crista bicipitalis is shorter than the crista deltopectoralis and gently curved.

The ulna has an elongate, slightly curved shaft and distinctly exceeds the humerus in length (Table 2.1). The olecranon is long and well developed. The condylus dorsalis ulnae and the condylus ventralis ulnae are well developed with a marked sulcus intercondylaris. Papillae remigales are not visible.

27 CHAPTER 2: PRIMOBUCCO KATIE DAVIS

The carpometacarpus is approximately half as long as the radius and is slender. The metacarpals are of equal length; the os metacarpale minus and the os metacarpale majus are straight. The spatium intermetacarpale is very narrow and the processus intermetacarpalis is very small. The proximal end of the os metacarpale minus bears a ventrally protruding projection, while the os metacarpale alulare is short and broad and its processus extensorius is large and protrudes cranially. The symphysis metacarpalis distalis is wide, the processus pisiformis is marked and the fovea carpalis cranialis is shallow. The phalanx proximalis digiti majoris is long and broad and lacks a large proximally directed process on the ventral side. The phalanx digiti alulae is also long and does not appear to possess a claw, in contrast to observations made by Mayr et al. (2004).

2.3.6 Ratios/measurements

The mean lengths of the humerus, ulna and carpometacarpus of each specimen in Table 2.1 were plotted to aid allocation of the new fossils to one of the Primobucco species. The graphs (Figure 2.3) show that there is a size distinction between the European species P. frugilegus and P. perneri , with the North American P. mcgrewi plotting at the lower end of the P. perneri range. For our new specimens FMNH PA 345 could only be plotted for humerus/ulna ratio and plotted in the same area as P. mcgrewi /P. perneri . FMNH PA 611 was a much larger specimen and plotted with P. frugilegus for all three sets of measurements.

Europe and North American have distinct avian faunas (Böhning-Gaese et al., 1998). Based on our knowledge of modern avian faunal distribution and the absence of migratory behaviour in modern rollers it seems unlikely that P. frugilegus would have been present in both Europe and North America or to have been migratory between the two geographic regions. Specimen FMNH PA 345 plots well within the P. mcgrewi range and it is reasonable, given the above, to conclude that specimen FMNH PA 611 is simply a larger specimen of P. mcgrewi than those previously known. There is no other evidence to suggest that the latter specimen requires a new species designation and therefore we assign both specimens to P. mcgrewi.

28 CHAPTER 2: PRIMOBUCCO KATIE DAVIS

34 33 32 31 30 29 Humerus 28 27 26 25 30 32 34 36 38 40 42 Ulna P. mcgrewi P. perneri P. frugilegus FMNH PA 611 FMNH PA 345 a/b

34 33 32 31 30 29 Humerus 28 27 26 25 10 12 14 16 18 20 Carpometacarpus P. mcgrewi P. perneri P. frugilegus FMNH PA 611

42

40

38

Ulna 36

34

32

30 10 12 14 16 18 20 Carpometacarpus P. mcgrewi P. perneri P. frugilegus FMNH PA 611

Figure 2.3: Biometric graphs showing mean limb ratios for species of Primobucco . All measurements are in mm and are taken from Table 2.1.

29 CHAPTER 2: PRIMOBUCCO KATIE DAVIS

2.4 Phylogenetic Analysis

The Primobucconidae have been considered to be closely related to either the Galbulae (Brodkorb, 1970) or the rollers (Houde and Olson, 1989). More recently, Mayr et al. (2003) placed the Primobucconidae as sister taxon to the extant and fossil rollers (). However, this study was limited, with only 16 taxa and 36 characters examined. New character information from these new specimens of Primobucco, together with data from the matrix supplied by Mayr et al . (2004), were added to the anatomical matrix of Mayr and Clarke (2003) in an attempt to place the Primobucconidae in a wider context. This matrix contains 47 taxa and 148 characters.

The matrix (Appendix E) was analysed following Mayr and Clarke’s (2003) methodology. As in their analysis three vertebral and sternal characters (55, 71 and 91) were ordered. The data matrix was analysed using PAUP* 4.0b10 (Swofford, 2002) using maximum parsimony. One thousand replicates of random stepwise addition (branch swapping: tree-bisection-reconnection) were carried out retaining only one tree at each step. A maximum of 10 trees one step longer than the shortest were retained in each replicate. Branches were collapsed to create soft polytomies if the minimum branch length was equal to zero.

2.5 Results

Analysis of the matrix resulted in 18 MPTs of length 721 (CI = 0.227, RI = 0.478, RC = 0.109). The strict consensus tree is shown in Figure 2.4. In the strict consensus the Primobucconidae are placed in a large polytomy at the base of the Neognathae minus Galloanserae. This unresolved position does not negate Mayr et al.’s (2004) conclusions drawn from their limited dataset, however it does not lend further support either. It is noticeable too that the tree produced by this study is significantly less well resolved than that of Mayr et al. (2004). The Adams consensus tree (Figure 2.5) shows that the Primobucconidae are “floating” in a clade that includes the Coraciidae but cannot resolve the relationships any further.

30 CHAPTER 2: PRIMOBUCCO KATIE DAVIS

Figure 2.4: Strict consensus of the 18 most parsimonious trees resulting from analysis of the matrix in Appendix E (length = 721, CI = 0.227, RI = 0.478, RC = 0.109).

31 CHAPTER 2: PRIMOBUCCO KATIE DAVIS

Figure 2.5: Adams consensus of the 18 most parsimonious trees resulting from analysis of the matrix in Appendix E (length = 721, CI = 0.227, RI = 0.478, RC = 0.109).

2.6 Discussion

Primobucco mcgrewi was first described by Brodkorb (1970) when it was placed in the family Bucconidae (puffbirds). The specimen consisted of only an incomplete right wing; therefore the description was necessarily limited. Feduccia and Martin (1976) created a new family, the Primobucconidae, and placed P. mcgrewi in this group, along with a number of other fossil birds. They considered the Primobucconidae to belong in the Piciformes and, within this, most closely related to the Bucconidae. More recently, Feduccia and Martin’s “Primobucconidae” has been shown to be a polyphyletic assemblage including stem-group mousebirds (Houde

32 CHAPTER 2: PRIMOBUCCO KATIE DAVIS and Olson, 1992; Mayr and Peters, 1998) and parrots (Mayr, 1998; Mayr, 2002). The only taxon originally placed in this family that remains there is P. mcgrewi , which, at the time, consisted of only the holotype (Brodkorb, 1970). Houde and Olson (1989) were the first to suggest that P. mcgrewi may belong with roller-like birds (Coraciiformes) and that other birds from the Green River Formation most closely resembled P. mcgrewi in morphology. Most recently, Mayr et al . (2004) have identified new specimens of P. mcgrewi and diagnosed two new species belonging to the Primobucconidae; P. perneri and P. frugiligeus . Their study described complete skeletons and conducted a cladistic analysis of the Primobucconidae. The analysis supports Houde and Olson’s (1989) suggestion of the inclusion of Primobucconidae within the Coraciiformes. Mayr et al. (2004) identified two supporting characters, one of which is also present in the new specimens described here (“carpometacarpus, os metacarpale minus with ventrally protruding projection on ventral side of proximal end”). The other character concerns the tarsometatarsus and is not preserved in our specimens. Mayr et al.’s (2004) analysis was unable to provide any resolution on the position of Primobucconidae within the Coraciiformes. The dataset used contained a relatively limited number of only 36 characters. Of these, a large proportion were concerned with the morphology of the skull and legs. The new specimens have enabled detailed descriptions of the shoulder girdle and wing morphology, which were lacking in Mayr et al.’s (2004) analysis. The specimens described here provide detailed descriptions and hence many cladistic characters that help fill the gap in our knowledge of this part of the of Primobucco . Despite not adding to our knowledge of the relationships of the Primobucconidae at this present time these new characters may eventually help us to elucidate relationships of this extinct taxon with the help of further new discoveries.

As Primobucconidae have been described from the Eocene of both North America and Europe (Mayr et al., 2004), while extant rollers have a distribution limited to the Old World, the confirmation of the affinities of the Primobucconidae is likely to have an impact on our understanding of the origins and evolutionary histories of extant taxa.

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Chapter 3

Supertrees of Galliformes: A test case for a supertree-building protocol

3.1 Abstract

This chapter extends previous work by other authors on arriving at a robust protocol for determining good quality input data for supertree analyses. This mostly involves looking at issues surrounding source tree independence and data integrity. Two methods of combining non-independent source trees are assessed in an attempt to identify the most appropriate method of dealing with duplicated data. The order Galliformes was chosen as a test case due to the comparatively small number of taxa, making it suitable for detailed analysis on a relatively short timescale, and well- documented monophyly of the group. The results of this study produced a robust protocol for collecting, storing and processing data ready for inclusion in a supertree analysis. Both methods produced reasonable supertrees that represent current views on galliform phylogeny, however, it was found that combining non-independent source trees via a “mini-supertree” analysis produced results more consistent with the input source data and, in addition, significantly reduced computational load.

3.2 Introduction

Criticisms of supertrees have arisen for a variety of reasons, both practical and philosophical. Data quality is the main practical issue (Gatesy et al., 2004) and is the main consideration of this chapter (see Chapter 1 for a full discussion of criticisms of supertrees in general) as the results can only be as good as the input data. In particular, a perceived, yet untested, problem with supertree analyses according to critics is the occurrence of weak, or poorly justified, data being included in supertree analyses (Gatesy et al., 2004) for example the inclusion of duplicated datasets which are non-independent. An example of between study non-independence would be the re-using of the same character set by several different authors in different publications. Within study non-independence can arise due to the production of

34 CHAPTER 3: GALLIFORMES SUPERTREE KATIE DAVIS several estimates of phylogeny using the same data, for example due to the use of a number of different tree-building methods, a well-known case being the placental mammal supertree of Liu et al. (2001) which contained a single transferrin immunology data set for bats that was incorporated into five different source trees. The outcome of including this dataset five times is that the immunology dataset is then effectively up-weighted by a factor of five. Further criticisms arise from the inclusion of source trees that can be considered to be appeals to authority (Gatesy et al., 2002). For example: source trees in which monophyly has been assumed and the topology accordingly constrained, source trees constructed from composite trees pieced together from previously published results, and source trees constructed from reviews of previous studies could all be classified as appeals to authority (Gatesy et al., 2002). Other criticisms are based on the potential for bias in the results dependent upon source tree properties. Wilkinson et al. (2005b) proposed that unbalanced trees are more likely to be represented in a supertree than their balanced counterparts when using standard MRP (Matrix Representation with Parsimony). Size has also been suggested to have an influence (Bininda-Emonds et al., 1999) and it is thought that larger source trees may “swamp” the dataset and therefore have a stronger influence on the resulting supertree than smaller source trees.

This chapter carries out a test study on a small group with well-documented monophyly, the Galliformes, in order to develop a protocol for selecting source trees. The approach is based on that designed by Bininda-Emonds et al. (2004), but resolves some of the issues with their protocol. The protocol developed here is subsequently used to construct the Aves supertree and a modified version is used to construct the Dinosauria supertree (Chapters 4 and 6 respectively).

3.3 Current Supertree Building Protocol

Many previous supertree studies have been rather ad hoc when it comes to data quality issues (e.g. Salamin et al., 2002; Davies et al., 2004; Thomas et al., 2004). Some authors have made attempts to minimise data duplication and other data issues. Ruta et al. (2003) in their supertree of early tetrapods evidently recognised the problems caused by duplicated data as they ran two separate analyses in an attempt to remove some non-independent data. Their first analysis included all collected source trees, while the second removed any that were superseded by subsequent

35 CHAPTER 3: GALLIFORMES SUPERTREE KATIE DAVIS analyses of similar datasets. Jones et al. (2002) also made an attempt by applying differential weighting to source trees in their bat supertree. These are clear attempts to improve source data quality but were not implemented in a rigorous manner. Bininda-Emonds et al. (2004) have been the first to propose a stringent protocol in an attempt to minimise data quality issues and to standardise supertree construction.

Bininda-Emonds et al.’s (2004) protocol was designed to deal with the data independence and quality issue, but as yet remains untested. It was used as a basis for a supertree of the Cetartiodactylia (Price et al., 2005) and the results were tested against a supermatrix, but the protocol itself was not tested in any way. Furthermore, Price et al. (2005) allowed the inclusion of informal phylogenies and two taxonomies. Therefore it was decided that before attempting a species-level supertree for all Aves, a strict protocol would be designed and tested. This protocol is based on that by Bininda-Emonds et al. (2004), but extends it and improves the practical aspects of it. In particular, although their protocol contains sensible ideas for source tree selection these are not backed up by any suggestions for implementation. As supertree analyses often contain large volumes of data some of the protocol stages are not easy to implement by hand or by eye and if attempted manually would likely be highly error-prone.

The following section gives a brief summary of the protocol of Bininda-Emonds et al. (2004) followed by the description of a revised and extended protocol intended for use in constructing a supertree of all Aves and tested here on the order Galliformes.

36 CHAPTER 3: GALLIFORMES SUPERTREE KATIE DAVIS

3.3.1 Summary of current protocol

Bininda-Emonds et al. (2004) identified the following factors to be considered:

1) Source tree independence

Possibly the single most important issue is concerned with the non-independence of data either between or within studies. An example of between study non- independence could be the re-using of the same character set by several different authors in different publications. Within study non-independence can arise due to the production of several estimates of phylogeny for the same data, e.g. due to the use of a number of different tree-building methods.

Also important here is the definition of “independent” source trees. Bininda-Emonds et al. (2004) define “independent” based on both the character data and taxa set.

Data considered independent:

• Non-overlapping datasets (e.g. different genes).

• Trees for non-overlapping taxa sets.

• Unique combinations of genes.

Data not considered independent:

• Trees derived from the same set of characters with the same taxa or where one taxa set is a subset of the other.

• Different portions of the same gene.

Figure 3.1 summarises Bininda-Emonds et al. (2004) suggestions on recognising independent source trees and how to deal with non-independence. Any sets of source trees that remain non-independent after processing can be combined by creating a “mini-supertree” to produce a summary of non-independent data, rendering it independent. These non-independent trees can therefore be represented in this way by a single independent source tree. This then removes any unnecessary up- weighting of source data. These “rules” have been challenged by other authors (Gatesy et al., 2004), who point out that there is still a lot of scope for character

37 CHAPTER 3: GALLIFORMES SUPERTREE KATIE DAVIS duplication. However, Bininda-Emonds (2004) does not consider this to be problematic as “duplication can occur at this level and still result in independent phylogenetic hypotheses because a phylogenetic tree is composed of more than the data going into it”.

All potential source trees

In different publications In the same publication • Independent data sources • Independent data • Unique combination of data sources sources in (1) • Unique combination of • Non-overlapping taxon sets data sources in (1) for the same data source • Non-overlapping taxon sets for the same data source

Otherwise

Independent Non-independent Otherwise source trees source trees

• Most comprehensive, then Independent Non-independent • Tree explicitly preferred source trees source trees by authors, then • Consensus of non- independent source trees (if present) Most recent and/or comprehensive, if superset of others Otherwise Otherwise

Independent Non-independent Independent Non-independent source tree set of source trees source tree set of source trees

Construct mini -supertree Construct mini -supertree

Representation of Representation of independent set of independent set of source trees source trees

Figure 3.1: Summary of protocol for selecting source trees. After Bininda- Emonds et al. (2004).

38 CHAPTER 3: GALLIFORMES SUPERTREE KATIE DAVIS

2) Standardisation of terminal taxa

Terminal taxa must be comparable throughout the source data and therefore should be standardised before undertaking a supertree analysis. Problems arise when taxa are not standardised as synonyms artificially inflate taxon numbers and potentially mask phylogenetic signal.

Bininda-Emonds et al. (2004) do use a script for automatic standardisation of terminal taxa – synonoTree.pl – however, it appears to work via a user-input list of names and is therefore still manually labour intensive and potentially error-prone as it will not pick up any synonyms or misspellings not already known to the user.

2.1) Combination of trees at different taxonomic levels

Taxa at different taxonomic levels must be incorporated into the tree in order to retain as much phylogenetic information as possible. However, it is important to standardise these taxa to a comparable taxonomic level in order to retain as much of the phylogenetic signal as possible. It is meaningless, for example, to include the taxon “Passeriformes” alongside members of that order as the software used to construct the supertree does not intrinsically “know” which taxa belong within that order. In the case whereby a higher-level name is to be used in supertree construction, Bininda-Emonds et al. (2004) recommend that all constituent lower- level taxa take on that name, although this approach does make an assumption regarding the monophyly of the higher-level taxon. When wishing to use lower-level names for supertree construction, Bininda-Emonds et al.’s (2004) first suggestion for dealing with higher taxa is to identify the actual taxa examined in the source study. This is evidently the desired solution; however this approach is not always feasible. Where it is not possible two potential solutions are suggested. The first is to assume monophyly of the higher taxon and to create an extra node consisting of all its constituent taxa. They acknowledge that this approach will artificially elevate support for monophyly of the higher taxon and, as such, this support is derived from an appeal to authority rather than from genuine evidence of monophyly. Their preferred option is to identify the type species of the higher taxon and use this as a substitute, suggesting that this makes fewer assumptions of monophyly and therefore potentially influences the resultant supertree topology to a lesser extent.

39 CHAPTER 3: GALLIFORMES SUPERTREE KATIE DAVIS

2.2) Accommodation of paraphyletic taxa

There are two instances in which paraphyletic taxa may present a problem. The first is the case of genuine paraphyly, whereby a taxon does not represent a monophyletic grouping. The second is where taxonomy has been standardised (see above – section 2.1) and two taxa, which were not in the original tree, considered to be each other’s closest relatives, become a single paraphyletic taxon in the standardised tree.

Both types of paraphyletic taxa need to be dealt with before inclusion in a supertree analysis as more than one node cannot have the same label within a tree, however both types of paraphyly can be dealt with in the same way.

Bininda-Emonds et al. (2004) recommended dealing with this scenario in one of two ways. Either a) where one of the paraphyletic taxa represents the type species this is taken as the reference species, or b) if this is not possible the position should be considered as uncertain and each source tree can be viewed as a number of different trees in which all the possible positions of the paraphyletic taxon are represented. These multiple source trees can then be dealt with in the same way as any other set of non-independent trees (Figure 3.2).

3) Source tree collection and selection

Bininda-Emonds et al. (2004) also point out the importance of careful source tree selection. They consider that only source trees based on original analyses should be considered valid and therefore collected. Any duplicated source trees as a result of secondary analyses should not be added to the dataset. They also suggest that it can be appropriate to include taxonomies in a supertree analysis but not other supertree analyses. In addition they recommend that only published source trees from reputable sources are collected.

Finally they state that all source trees to be included in an analysis should be collected as they appear in the source publication and thereafter modified to suit the particular supertree analysis to be performed.

40 CHAPTER 3: GALLIFORMES SUPERTREE KATIE DAVIS

Figure 3.2: X and Y are the same species “Z”, which renders Z paraphyletic in tree (a). One solution is to prune each of the source species to produce a set of source trees reflecting the uncertain position of Z (b). If two or more source species of Z form a monophyletic clade (W and X in tree (a)), this clade can be collapsed to a single terminal (c). After Bininda- Emonds et al. (2004).

3.4 Methods

The following proposed protocol is based on the above-described by Bininda- Emonds et al. (2004) but with a number of additional steps and methods of practical implementation. The data processing was split into individual stages, each of which dealt with a single issue. The stages were:

1. Data collection and entry (section 3.4.1).

2. Source tree independence (section 3.4.2).

3. Standardisation of terminal taxa (section 3.4.3).

4. Combination of trees at different taxonomic levels (section 3.4.4).

5. Accommodation of paraphyletic taxa (section 3.4.5).

41 CHAPTER 3: GALLIFORMES SUPERTREE KATIE DAVIS

6. Data integrity check (section 3.4.6).

7. Check adequate overlap of source trees (section 3.4.7).

8. Matrix creation (section 3.4.8).

With all these steps completed, the data will be in a state such that it is ready to be input into a supertree analysis. This protocol will also then be used to create a species-level supertree of Aves.

The main unanswered question is whether it is best to deal with non-independent source trees via combination into a “mini-supertree” (“method A” as suggested by Bininda-Emonds et al., 2004) or by the appropriate weighting of source trees to avoid unintentional “up-weighting” of non-independent trees (“method B”). This question will be investigated and resolved as a part of this chapter (section 3.4.2).

3.4.1 Data collection and entry

Potential source trees were identified initially from online resources. The Web of Science 1, Science Citation Index was searched; covering the years 1981 to 2005. Papers potentially containing trees were examined. The reference lists within these papers were then searched for papers containing trees. All papers containing trees were retained and this process was continued until as many trees as possible were found. Papers were collected up to the end of December 2005 as at that point data processing commenced. A total of 589 papers were collected for the large Aves dataset that were deemed to contain potentially useful source trees, of these 39 were suitable for inclusion in this small test study. The majority of the relevant source trees were collected, but there is a great wealth of information regarding avian phylogeny and it is always possible that some have been missed. Reasons for source tree exclusion included the lack of cladistic methodology, i.e. trees drawn by hand or inferred from a taxonomy, use of a non-original tree, the use of a summary tree created from previous trees, and source tree non-independence. Bininda-Emonds et al. (2004) consider that it can be appropriate to include taxonomies and informal phylogenies in supertree analyses, and indeed have done so (e.g. in Price et al.,

1 http://wok.mimas.ac.uk

42 CHAPTER 3: GALLIFORMES SUPERTREE KATIE DAVIS

2005), however it was decided that as they are only summaries of phylogenetic knowledge, and therefore not derived from primary sources, that it would not be appropriate to include them in this analysis.

Diligent data entry and recording is of utmost importance as it ensures that all steps of data processing remain completely transparent. It also allows for easy identification of errors as all changes to the original data can be recorded during data processing. Crucially, when done in a consistent and sensible manner, it also leaves an audit trail for other researchers to enable further updates to the tree in future.

Data entry proceeded by converting each source tree into a Nexus format tree file (using the software TreeView 1.6.6, Page, 1996). In addition to this, each tree was accompanied by a XML file containing metadata about each source tree, such as source information, i.e. authors, journal, year etc., included taxa, and character information. This was to ensure that no information about the source data was lost during processing and ensures a consistent standard of data collection throughout. This format was chosen, rather than simply creating a document in Word or Excel, as it is very easy to extract trees required for any specific analysis, i.e. morphological or molecular data only or extant taxa only, by parsing the XML. A Java tool, which is available online 2 (Hill, pers. com.), was used to facilitate ease of data entry and ensure consistency of the XML files (see Figure 3.3). New data can also be easily added, an important factor as new phylogenies are constantly being published. It would even be possible to add other types of information if required at a later stage. The structure would also allow other workers to reconstruct exactly the steps taken here, or to investigate other possibilities, for example by only selecting data that are based on morphology. In addition, these files were later used to allow checking of data independence, substitution of higher taxa and gathering various statistics on the data by the use of various Perl scripts (see Appendix F).

The input data for the supertree essentially consist of tree files in Nexus format, which contain the taxa and phylogenetic relationship of the input tree. These are essentially all that is needed to construct a supertree. However, as discussed above,

2 http://www2.epcc.ed.ac.uk/~jon/

43 CHAPTER 3: GALLIFORMES SUPERTREE KATIE DAVIS useful metadata can also be stored alongside these trees in the form of XML files. In order to organise the data, each paper that contained one or more source trees had a corresponding folder created which was labelled in the form of Author_Author2_Year. If more than two authors were listed, "etal" was used for Author2. Within each of these author folders, a further folder was created for each tree within the paper. The tree file and an accompanying XML file were then created within these folders. The result is a nested set of folders that have a predictable name and contain all data necessary to both construct a supertree and process the data further. This method proved much more efficient than that utilised in a previous project (Davis, 2003) which involved inputting trees by hand into Excel – a much more cumbersome and error-prone method.

Figure 3.3: Screenshot of BirdXML; a Java client for easily creating the XML files.

All stages of source tree processing were retained in order to provide transparency should it be necessary to see what steps were carried out at an earlier stage.

3.4.2 Source tree independence

By and large, the suggestions made by Bininda-Emonds et al. (2004) were carried out as suggested (see Figure 3.1). However, the incorporation of non-independent

44 CHAPTER 3: GALLIFORMES SUPERTREE KATIE DAVIS sets of source trees via a mini-supertree analysis rather than by a method such as down-weighting the trees is not intuitive and has yet to be tested for validity. One concern is that combining source trees using Matrix Representation with Parsimony (MRP) could be taking the data a step even further away from the original. It could be argued, however, that supertrees are already removed from the original data and therefore any inaccuracies introduced by combination of source trees by MRP will be negligible. In this study these two methods will be compared and contrasted. Two separate supertrees of Galliformes will be built, the difference being in the way in which non-independent source trees are dealt with. One method (A) will take non- independent source trees and combine them into “mini-supertrees” using MRP, the other (method B) will down-weight them by an appropriate amount to remove any inappropriate up-weighting of character data. Comparisons to evaluate each method will be carried out using ent (Page, pers comm) and looking at two metrics – MASTd (Maximum Agreement SubTrees) and triplets – to investigate how well each supertree represents the source tree and whether one method outperforms the other. MAST compares each input tree to the supertree and calculates the ratio of leaves that appear in the same position in both trees to the total number of leaves in the input tree (Chen et al., 2001). A perfect match is where the whole input tree is reproduced in the supertree and would score 1. If half of the leaves appeared in the same position, the score would be 0.5. Triplets are the rooted equivalents of quartets. For each input tree “T” that tree is compared with the subtree of the supertree that results when any taxa not in “T” are pruned. For any pair of triplets (one from each tree) there are five possible outcomes: a) the triplets are resolved in both trees and are identical, b) the triplets are resolved in both trees and are different, c) the triplet is resolved in one tree, or the other (d), but not both, and e) the triplet is unresolved in both trees. For the purpose of these comparisons only a), b) and d) are relevant. From these a score is calculated for each triplet pair using equation 1 (Page, 2002).

fit = 1− (d + r2) (1) (d + s + r2)

Here, d is the number of triplets resolved differently in tree 1 and tree 2, s is the number of triplets resolved identically in tree 1 and tree 2, r1 is the number of triplets resolved in tree 1 but not in tree 2, and r2 is the number of triplets resolved in tree 2 but not in tree 1.

45 CHAPTER 3: GALLIFORMES SUPERTREE KATIE DAVIS

Before any of this could be implemented it was important to define what is meant by an “independent” source tree for the purpose of this study. For the purpose of this study source trees were considered to be independent or not according to the following criteria.

Data considered independent:

• Trees with non-overlapping datasets (e.g. different genes/different morphological characters).

• Trees for non-overlapping taxa sets.

• Unique combinations of genes.

Data not considered independent:

• Trees derived from the same set of characters with the same taxa or where one taxa set is a subset of the other. In this instance, trees were only considered non-independent if they shared all taxa or if one set was contained entirely within another. Trees from the same characters that shared some taxa, but not all were considered independent.

• Different portions of the same gene.

Non-independent trees were identified using a Perl script (Appendix F: check_independence.pl) that implemented the above rules. The script looks at the metadata and compares both the analysis type and character data. If the same characters and analysis are used within studies, the script checks the taxa list. If this is the same, the files are flagged as potentially non-independent. For each input tree file a list of tree files is given that are potentially non-independent. The script is designed to be pessimistic in judging independence. If there is doubt over the dependency of source trees, they are flagged as non-independent. The decision of dependency is then left to the user. The non-independent trees are then either a) removed if they are redundant (i.e. contained entirely within another dataset, not an original study or not a valid source tree for any other reason), or b) combined into a mini-supertree.

46 CHAPTER 3: GALLIFORMES SUPERTREE KATIE DAVIS

For method A combined trees were created using PAUP* 4.0b10 (Swofford, 2002) to make a “mini-supertree” of all the relevant overlapping source trees. In the vast majority of cases it was possible to use the “branch and bound” option for creating the trees, only a small number required “hsearch”. In the case where PAUP* 4.0b10 (Swofford, 2002) found multiple MPTs (most parsimonious trees) a strict consensus was computed. These combined trees were then used in the analysis as independent source trees.

For method B trees were appropriately weighted (i.e. four synonymous trees were each given a weight of 0.25) in order to consider relations of non-independence among the input trees (Gatesy et al., 2002; Bininda-Emonds et al., 2004). In order to avoid the problem of weights being represented as floating point decimals (i.e. 0.33 x3 ≠ 1 due to rounding errors) weights were initially worked out as a fraction of 1 but then the common factor was calculated and then all the weights were multiplied by this figure resulting in all weights being represented by integers. In this case the common factor was found to be 12 and therefore all independent trees carry a weight of 12 and down-weighted trees have various values dependent upon the number to be combined.

3.4.3 Standardisation of terminal taxa

It is necessary that terminal taxa be standardised in order to eliminate synonyms/misspellings, paraphyly in taxa and also to ensure that all taxa are represented at the same taxonomic level. Synonyms and misspellings are a major problem in avian taxonomy so this step is vital. The existence of non-standardised terminal taxa creates problems when constructing phylogenies as any given species may be known by very different names depending upon which classification is used. Many misspellings are also in existence, some have been perpetuated throughout the scientific literature accumulating yet more misspellings until they are almost unrecognisable from the original name. It is possible, even likely, that many ornithologists would disagree on the “correctness” of the names used in this thesis. However, the ultimate aim was to standardise the taxonomy and therefore it is more important that synonyms/misspellings/vernacular terms are identified and removed and less important that the names used as the standard are universally agreed upon. It

47 CHAPTER 3: GALLIFORMES SUPERTREE KATIE DAVIS is probably useful to think of this as a process of standardising taxonomy rather than one of taxonomic correction .

Bininda-Emonds et al. (2004) did not suggest any practical means of standardising terminal taxa so, bearing in mind that the Galliformes supertrees and the subsequent avian supertree were to be constructed at species-level, the following steps were taken:

• Taxa lists as found in published phylogenies were loaded into the Glasgow Taxonomic Name Server 3 (Page, 2005), which then returned the list corrected for any possible synonyms/misspellings. The Name Server was developed by Prof. R. D. M. Page and checks input names against those held in the database in an attempt to identify synonyms/misspellings of names.

• On occasions the name server identified an unrecognised name but was unable to suggest an alternative. In this situation the name was searched for in the Taxonomic Search Engine, which searches five databases (ITIS, Index Fungorum, IPNI, NCBI and uBIO) (Page, 2005). Any hits were then investigated and the correct name identified in this manner.

• As a last resort, names that did not appear in the Name Server or in any taxonomic database were input into Google 4 and search results investigated. It was usually the case that the name had been misspelt so badly that it was not recognised by the Name Server but could be identified by a process of elimination, some prior knowledge of the taxon in the question, and knowledge of common misspellings in avian taxonomy. For example the common endings of specific names “–a” and “–us” are often mixed up, i.e. flava/flavus , also the addition/subtraction of extra vowels as in reevesi/reevesii.

• The new taxa list was then used to create a new tree for the source phylogeny using TreeView 1.6.6 (Page, 2001). The standardising of names often

3 http://darwin.zoology.gla.ac.uk/~rpage/MyToL/www/index.php

4 http://www.google.co.uk

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resulted in paraphyly of previously monophyletic taxa, although sometimes the reverse was the case. In the former situation the paraphyletic taxa were dealt with as detailed in this section, point 4. The original tree direct from the source phylogeny was also retained, recorded exactly as in the source, both for completeness but also in order to enable further exploration into issues in avian taxonomy in the future.

It is accepted that there are still likely to be inconsistencies in the taxonomy used here, therefore a complete list of those synonyms/misspellings not found by the Glasgow Taxonomic Name Server, and the taxa they were deemed to be, is provided in Appendix A.

In some instances the name server allowed two variations of a single name, e.g. Gallus sonnerati /G. sonneratti . In this scenario the Howard and Moore (2003) checklist was consulted and the name given in there was used. In trees where vernacular names were used (e.g. Sibley and Ahlquist, 1990 – operational taxonomic units (OTUs), “New World ” and “ and turkeys”), Howard and Moore (2003) was also used. This checklist was chosen as the default position as it represents a conservative view of avian taxonomy. It was important to take a conservative view, as this is likely to invoke fewer assumptions that could be regarded as appeals to authority, such as regarding monophyly of higher taxa or the belonging of a particular taxon to a given group.

3.4.4 Combination of trees at different taxonomic levels

Where terminal taxa were referred to by a higher-level name (genus or higher) it was attempted to identify the particular species used in the analysis, in order to avoid unjustified assumptions of monophyly, and these were then coded into the tree. Where this was not possible, all members of that higher taxon were coded as a star polytomy, but only where those taxa were already present elsewhere in the supertree analysis. Bininda-Emonds et al. (2004) suggest inserting the type species, but it was felt that this made too strong an assumption as the original tree is not stating that just one species is present in that node but that all species in that higher taxon are present.

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One exception to this substitution rule has been made in the case of species and sub- species. Sub-species are used much less frequently in analyses than species. Although it is desirable to make no changes to the original source tree, the adding of all known sub-species in the form of star polytomies in source trees in which only the species name is given would be cumbersome, unnecessarily increase computational time and then add little or no value to the resulting estimate of phylogeny (Pisani et al., 2002). Although in some instances species can be shown to be paraphyletic (this issue is dealt with separately – see stage 5) the case for standardising all taxa at the species level far outweighs the evidence in favour of this approach. The second, and final, exception is in the case where species belonging to a higher taxon are not actually present in any of the source trees. No examples of this were present in the Galliformes dataset, but in the Aves species-level tree there exists a fossil family – Zygodactylidae (Mayr, 2004) that was left in the dataset at family-level rather than substituting the constituent taxa. All taxa falling into this category were left as higher taxa in order not to artificially inflate taxa numbers.

To facilitate an easy method for substituting higher taxa a Perl script (Appendix F: replace_higher_taxa.pl) was written to automate the process. Briefly, the script performs the following operations:

1. Scan all XML data to create a list of unique taxa.

2. Create a list of higher (than species) taxa by assuming any taxon which contains only a single word is a higher taxon.

3. If a species (i.e. a taxon consisting of two words – subspecies have already been removed) in the taxa list matches a higher taxa, add it to the substitution list. For example, if “ Gallus ” is found in the taxa list, then it becomes a “higher taxon”. Then if “ Gallus gallus ” is found, this is added to the list to be substituted for “ Gallus ”. Additionally, if “ Gallus varius ” is also found, “Gallus ” will now be substituted with “ Gallus gallus ” and “ Gallus varius ”. Note that the user can also input this list of substitutions if required (see below).

4. Go through all tree files and XML files performing the necessary substitutions depending on the following:

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a. If a species in the substitution list already exists in the tree, do not substitute this species in this particular tree.

b. If the substitution is empty (i.e. because all the species belonging to that higher taxa are already in the tree) remove the higher taxon.

5. The substituted higher taxon is replaced by a polytomy.

6. Overwrite the existing files with the updated tree and XML data.

In step 3, the list generated makes the assumption that taxa with a single word as a label are generic names and taxa with two words as a label are specific names. This may not always be the case as, for example, there may be family or informal names within a tree (e.g. Sibley and Ahlquist, 1990 contains “pheasants and ” and “New World quails”). To resolve these cases, the user can specify substitutions that should be made via an optional input file. This can also be used to remove unwanted taxa (e.g. MRPOutgroup from combined mini-supertrees) very easily by specifying an empty substitution.

The replacement of higher taxa can take place in several stages, which assists verification of the substituted data, allows taxa that are higher than generic names to be replaced with generic names before being substituted with specific names, and removes unwanted taxa before any subsequent processing.

As in the case for synonyms, Howard and Moore (2003) was used to define inclusion of species within higher taxa, for the same reasons given above (section 3.4.3).

3.4.5 Accommodation of paraphyletic taxa

To accommodate paraphyletic taxa all possible permutations of the taxon’s position were created in separate tree files, then all these trees were combined into a mini- supertree.

In order to create the trees containing all possible permutations of paraphyletic taxa the Nexus file was modified slightly. All paraphyletic taxa were input as the corrected taxon name with the characters %n, where n is an integer starting from one, appended onto the end. For example if the species Aerodramus spodiopygius

51 CHAPTER 3: GALLIFORMES SUPERTREE KATIE DAVIS appears in two locations within a tree, e.g. by removing a subspecies or after standardising a name, these are labelled as 'Aerodramus spodiopygius%1 ' and 'Aerodramus spodiopygius%2' . A Perl script (Appendix F: tree_permutation.pl) was then used to scan for names with the tagging characters, shuffle the taxa such that only one taxon from each paraphyletic group was contained in the tree, and save the resulting tree. A recursive function ensured that all possible permutations of paraphyletic positions were covered. This approach also worked in the terminal taxa standardisation stage in the case when paraphyletic subspecies needed to be removed.

Once all permutations were realised, a “mini supertree” was constructed, ensuring data independence.

3.4.6 Data integrity check

The data integrity between the tree files (Nexus text file) and the XML metadata is a key component of the dataset. The idea of using two separate files may seem unwieldy, but allows cross-checking of one against the other on common data to allow errors created during editing of one or both to be caught. To make testing easier, a short script (Appendix F: check_integrity.pl) which performs three checks was written. The first check is on the XML files, to ensure their validity. This is very simple to carry out and the XML parser will spot most errors. If an XML file contains an error, it is flagged to the user for checking. It could be made more robust by using Document Type Definition (DTD), but this was considered too high an overhead on this project as the XML may have been extended and/or altered. The next check was to ensure validity of the tree files. All the tree files encoded in this project were in "translated" format (see Box 3.1). An easy check for syntax errors is to translate the tree to normal nexus format (see Box 3.2). If the translation fails, the tree is flagged as possibly erroneous. Finally, the cross-check between XML and tree files checks that the same taxa are contained in both for each pair of files. The script checks that the same number of taxa are present in both files and then checks each taxon against the other file. If there are differences, these are flagged to the user to inspect.

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#NEXUS BEGIN TAXA; DIMENSIONS NTAX = 4; TAXLABELS Taxon_w Taxon_X Taxon_y Taxon_z ; ENDBLOCK; BEGIN TREES; TRANSLATE 1 Taxon_w 2 Taxon_x 3 Taxon_y 4 Taxon_z ; TREE * tree_1 = (1,2,(3,4)); ENDBLOCK;

Box 3.1: Example tree in translated Nexus format.

#NEXUS BEGIN TREES; TREE * tree_1 = (Taxon_w,Taxon_x,(Taxon_y,Taxon_z)); ENDBLOCK;

Box 3.2: Example tree in standard Nexus format.

3.4.7 Check adequate overlap of source trees

This step is missing from the Bininda-Emonds et al. (2004) protocol, but is a fundamental requirement of constructing a supertree (Sanderson et al., 1998). Each source tree must share at least two taxa with at least one other source tree in order to be included. Connections between sources trees were determined by a Perl script (Appendix F: tree_cluster.pl). Floating source trees that are not connected to any others and also “islands” of connected source trees (those that share two or more taxa between them, but do not join on to the main group of source tree) should also be eliminated. Figure 3.4 shows a graphical method of determining this using

53 CHAPTER 3: GALLIFORMES SUPERTREE KATIE DAVIS

GraphViz 5. A node represents each source tree and edges are created between nodes when two or more taxa are shared between the corresponding source trees. The small island of trees 6, 7, 8 and 19 should be removed.

It was ensured that the source trees fulfilled the minimum requirement of overlap with other source trees (at least two taxa with at least one other source tree) before the trees were considered ready for the supertree analysis

Figure 3.4: Graphical representation of minimal overlap of source trees (example from Chapter 5). Each node represents a source tree and edges represent an overlap of at least two taxa between those nodes. The island consisting of four source trees 6, 7, 8 and 19 should be removed from the study.

5 http://www.graphviz.org

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3.4.8 Matrix creation

After all data processing there remained a total of 53 source trees from a total of 39 source references to be included in the analysis. There were a total of 202 taxa included in the analysis. See Appendix B for a list of source references.

First trees were combined into a single file (Appendix F: amalgamate_trees.pl), then MRP matrices for both datasets were created using a version of Bininda-Emonds’ SuperMRP.pl Perl script (Bininda-Emonds et al., 2005) which was modified to run in Windows. See Appendix E for the MRP matrix.

3.5 Analysis

Both datasets were run in PAUP* 4.0b10 (Swofford, 2002) using the Parsimony Ratchet (Nixon, 1999). A script of Bininda-Emonds (perlRat.pl 6) was used to create the ratchet command file. The default parameters run 5 batches of 200 iterations. This was increased to 10 batches of 500 iterations in order to increase the chances of finding the shortest tree. The matrices were also run in TNT (Goloboff et al., 2008) using the “xmult=level 10” command; an aggressive search designed to find the shortest trees. An attempt was also made to utilise POY (Varón et al., 2007), as this is another recently developed piece of software for analysis of phylogenetic data, however POY requires 714Mb just to load the weighted Galliformes dataset and simple processing of the file uses 1.5Gb, which crashes the system.

Searches were carried out on an Apple MacBook 2.0GHz Intel Core 2 Duo with 2GB of RAM.

The resultant supertrees were compared to the source trees in order to assess fit and therefore which, if either, of method A (combining source trees) or method B (weighting source trees) provided better results. The program ent (Page, pers comm) was used for this. Ent compares the output (the supertree) to all the input trees (the source trees) and gives scores for each input tree (scores are between 0 and 1 with 0 being a complete mismatch and 1 being a perfect match).

6 http://www.personal.uni-jena.de/~b6biol2/ProgramsMain.html

55 CHAPTER 3: GALLIFORMES SUPERTREE KATIE DAVIS

3.6 Results

3.6.1 Galliformes supertrees

The shortest trees found by TNT (Goloboff et al., 2008) were significantly shorter than the shortest trees found in PAUP* 4.0b10 (Swofford, 2002) using the Parsimony Ratchet (Nixon, 1999) for both datasets. For the combined data the Parsimony Ratchet found 178 MPTs of length 988, TNT found 8 MPTs of length 961. For the weighted data the Parsimony Ratchet (Nixon, 1999) found 220 MPTs of length 12458, whilst TNT found 17 MPTs of length 11912. The majority-rule consensuses of the trees found by TNT are shown in Figure 3.5 (combined supertree) and Figure 3.6 (weighted supertree).

The two trees are broadly similar and show essentially the same higher-level relationships. Both are concordant with generally accepted views of galliform phylogeny. The fossil taxon Paraortygoides (two species) is placed as the sister taxon to all extant Galliformes. The extant families are not all monophyletic but do broadly fall into the pattern of (Megapodiidae, (, (Numididae, (Odontophoridae, (, (, (Tetraonidae))))))).

Megapodiidae and Cracidae are resolved as monophyletic groups with the exception of Penelope superciliaris in the combined tree, which is placed as the sister taxon to Galliformes minus Megapodiidae and Paraortygoides. This is not supported by any of the source trees and, as such, can be considered to be a spurious result. Megapodiidae and Cracidae do not, however, form the monophyletic taxon Craciformes as proposed by Sibley and Ahlquist (1990). Instead, the supertree supports the more traditional view of the Megapodiidae forming the sister group to all other extant Galliformes (as in Dimcheff et al., 2002; Dyke et al., 2003; Gulas- Wroblewski and Wroblewski, 2003; Smith et al., 2005).

A paraphyletic Numididae and monophyletic Odontophoridae are sister taxa to a monophyletic Phasianidae, which contains the majority of galliform species. In the combined tree the Numididae are rendered paraphyletic only by the grouping of niger with the fossil taxon Gallinuloides wyomingensis. In the weighted tree it is the inclusion of the taxon lathami within the Numididae that

56 CHAPTER 3: GALLIFORMES SUPERTREE KATIE DAVIS causes the paraphyly. Neither of these relationships is present in any source tree, however in Dyke and Gulas (2002) F. lathami (along with other taxa) and the Numididae taxa are all present as part of the same large star polytomy, this could cause F. lathami to spuriously cluster with the Numididae. The fossil taxon Gallinuloides wyomingensis is placed as the sister taxon to Phasianidae + Odontophoridae + Numididae in the weighted tree, as suggested by Dyke (2003).

The Phasianidae is a large order and it is easier to consider the individual subfamilies that it comprises. Subfamilies have been defined according to Howard and Moore (2003) in keeping with earlier definitions for higher taxa within this chapter. Using this classification, the Phasianidae contains a paraphyletic (Old World ) and (pheasants). Pheasants and partridges were originally thought to represent monophyletic lineages (Johnsgard, 1986, 1988; Sibley and Ahlquist, 1990), however, more recent evidence (Kimball et al., 1999; Geffen and Yom-Tov, 2001; Smith et al., 2005) suggests that this is not actually the case. The supertrees are concordant with the non-monophyletic viewpoint. Within the Perdicinae the are split into the francolins and francolins as suggested by Crowe et al. (1992) and Bloomer and Crowe (1998) but are not monophyletic (as found in Bloomer and Crowe, 1998). The partridge francolins form a sister group to the quails, Madagascar partridge ( Margaroperdix madagarensis ) and to the partridges, again as in Bloomer and Crowe (1998). The Phasianinae are roughly split into two groups; a monophyletic group containing the and allies, and ; and a paraphyletic group containing the gallopheasants and allies, and the .

The monophyletic Meleagridinae (turkeys) and Tetraonidae () are each other’s closest relatives and cluster with the branch of the Phasianinae containing the gallopheasants and tragopans (as in Geffen and Yom-Tov, 2001; Dimcheff et al., 2002). Kimball et al. (1999) support the clustering of the Meleagridinae and Tetraonidae but are not able to resolve the relationship of these to other Phasianidae.

57 CHAPTER 3: GALLIFORMES SUPERTREE KATIE DAVIS

Figure 3.5: Combined supertree – shown is the 50% majority-rule consensus of 8 MPTs of length 961, found in TNT (Goloboff et al., 2008).

58 CHAPTER 3: GALLIFORMES SUPERTREE KATIE DAVIS

Figure 3.6: Weighted supertree - shown is the 50% majority-rule consensus of 17 MPTs of length 11912, found in TNT (Goloboff et al., 2008).

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Comparisons were made between the resulting supertrees and the set of source trees to assess the suitability of the two methods of dealing with overlapping data. As the data do not follow a Gaussian distribution (see Figure 3.7), a non-parametric test must be used to ascertain if the difference between the weighted and combined fit scores are statistically significant. Therefore the Mann-Whitney-U test was used to test if the difference between the means of the two samples was statistically significant.

Combined MASTd Score Weighted Triplet Fit

16 10 14 9 8 12 7 10 6 8 5 4 Frequency Frequency 6 3 4 2 2 1 0 0 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 MASTd Score Fit Score

Weighted MASTd Score Weighted Triplet Fit

30 25

25 20 20 15 15 10 Frequency 10 Frequency

5 5

0 0 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 MASTd Score Fit Score

Figure 3.7: Histograms of fit scores for both combined and weighted methods. Note that neither method produces a Gaussian distribution (which is desirable as the optimum fit would be all trees with a score of 1 and hence give a non-Gaussian distribution).

The results show that for the combined dataset the mean fit scores are 0.37 for triplet fit and 0.45 for MASTd (higher score indicates better fit). For the weighted dataset the mean fit scores are 0.23 for triplet fit and 0.37 for MASTd (see Table 3.1) for full statistics). From these scores (Table 3.1) and the box plots (Figure 3.8) the combined supertree appears to be a better fit (higher mean score) to the source trees than the weighted supertree. To test if this is significant, the Mann-Whitney-U test was used, which showed that the higher mean fit for the combined dataset is statistically significant to a 0.99 confidence level for both MASTd and triplet fit. The calculated

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P-value of 0.0104 is statistically significant; and shows that there is a significant difference between the means of the two samples.

Table 3.1: Statistical data for “fit” scores for both combined and weighted methods.

Method Min 1st Qu Median Mean 3rd Qu Max.

Weighted Triplets 0.00 0.11 0.19 0.23 0.35 0.64

Combined Triplets 0.00 0.11 0.30 0.37 0.63 1.0000

Weighted MASTd 0.12 0.28 0.35 0.37 0.44 0.71

Combined MASTd 0.15 0.32 0.43 0.45 0.55 0.90

MASTd Triplet Fit

1 1 0.9 0.9 0.8 0.8 0.7 0.7 0.6 0.6 0.5 0.5 0.4 0.4 Fit score Fit 0.3 score Fit 0.3 0.2 0.2 0.1 0.1 0 0 Combined Weighted Combined Weighted n = 53 n = 81 n = 53 n = 81

Figure 3.8: Box and whisker plots for combined and weighted data (see Table 3.1).

In addition to this, the time taken for each tree to compute was recorded (see Table 3.2). It was found that the combined dataset ran much more quickly in both programs. Therefore, combining non-independent source trees is much more efficient and saves significant computing time compared to weighting input trees, by running in just 60% of the time it takes to complete the weighted dataset when using the Parsimony Ratchet and 64% of the time when using TNT. In addition, TNT runs in just 12% of the time taken by the Parsimony Ratchet for both datasets. Yet

61 CHAPTER 3: GALLIFORMES SUPERTREE KATIE DAVIS another advantage of combining non-independent trees rather than applying differential weights was that it was much quicker and easier, when processing the data, to combine trees into mini-supertrees than it was to allocate weights and to create a weight set.

Table 3.2: Statistical data for “fit” scores for both combined and weighted methods

PAUP (Parsimony Ratchet) TNT

Combined 26 min 15.886 secs 3 min 14 secs

Weighted 43 min 29.463 secs 5 min 2 secs

3.7 Discussion

Both supertrees gave reasonable, sensible results with a minimum of spurious groups. There were no surprises in the results and both conformed well to currently accepted views on galliform phylogeny.

There was a statistically significant difference between combined and weighted methods to a 0.99 confidence level. Two scoring methods were used in order to provide a more robust test. These scoring methods are independent of each other and still gave the same result. This increases confidence in the result that combining non- independent data gives a supertree more consistent with the source data than by applying differential weights for this dataset.

Weighting of non-independent source trees seems more intuitive, however, as shown above; combining source trees gives results more consistent with the input data. Also, there are potential issues with any original weights of the source trees although this is only on a small scale and therefore relatively unimportant. Additionally, the weighted dataset takes longer to calculate and it can be tricky to load weighted data into some software (e.g. POY, TNT) without manual work. It is important for data to be as portable as possible to allow collaborative methods of tree-building (see Chapter 4) so that the matrix can be tested on as many different types of software as possible.

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In addition to being statistically shown to produce a tree more compatible with the source trees than via weighting non-independent source trees, combining trees is much more convenient and allows utilisation of a wider variety of types of analysis, such as TNT (Goloboff et al., 2008) and POY (Varón et al., 2007) which have much more powerful algorithms than PAUP* 4.0b10 (Swofford, 2002). This method will be utilised for the main Aves dataset, which will be analysed in TNT, as this has been shown to consistently find the shortest trees in the shortest timescales. Run time and speed become increasingly important as datasets become larger so whilst a difference of a scale of minutes or 10s of minutes may seem unimportant on a dataset of this size, it has the potential to make a huge difference in the time taken to find the shortest trees on a much larger dataset.

3.8 Conclusions

The aim of this chapter was to develop and test a protocol for supertree construction using the Galliformes as a test case and with the ultimate aim of creating a robust protocol suitable for the construction of a supertree of Aves. This protocol was based on that outlined by Bininda-Emonds et al. (2004) but modified and extended, and tested on real data. The use of Perl scripts to automate data processing wherever possible greatly increases efficiency and reduces errors. This increased efficiency and reduction of errors will be even more vital for constructing a species-level supertree of Aves (see Chapter 4).

Several areas were identified that had not fully been explored by Bininda-Emonds et al. (2004); these were largely practical issues that had no clear implementation. These issues were resolved, often by the use of automated scripts, which had the dual effect of reducing error and also increasing efficiency. However, the greatest issue was whether to combine (via mini-supertree) or appropriately weight non- independent source trees. It was found that combining non-independent source trees produced a supertree that had a significantly higher mean fit to the original source trees than that produced by weighting of source trees. In addition, the combined datasets were much quicker to run in both programs, PAUP* 4.0b10 (Swofford, 2002) and TNT (Goloboff et al., 2008), than the weighted dataset, and TNT was substantially quicker to run each dataset to completion than PAUP*4.0b10.

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The supertrees were very similar in terms of large-scale relationships. Both gave sensible results and only a small number of spurious groups were identified. Neither tree should be regarded as a definitive representation of Galliformes phylogeny in any way but more as a summary of current knowledge.

Given the above discoveries and results, the species-level avian supertree, that is the main aim of this thesis, will be constructed as per the protocol developed in this chapter and via the combining of source trees to remove data non-independence.

The next chapter deals with the construction of the species-level avian supertree and explores the issues arising from the assembly of a supertree on such a large scale.

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Chapter 4

A species-level supertree of Aves

4.1 Abstract

Supertrees are a useful method of constructing large-scale phylogenies by assembling numerous smaller phylogenies that have some, but not necessarily all, taxa in common. Supertrees have been produced for a diverse range of taxa including dinosaurs, mammals and crocodiles. Birds are an obvious candidate for supertree construction as they are the most abundant land vertebrate on the planet and no comprehensive phylogeny of both extinct and extant species currently exists. Here, a species-level supertree has been constructed containing over 5000 taxa from over 700 source trees. The tree shows the relationships between the main avian groups, with only a few novel clades, most of which can be explained by a lack of information regarding those taxa. The tree was constructed using the strict protocol described in Chapter 3, which ensures robust, accurate and efficient data collection and processing. In addition, the tree was constructed in a collaborative fashion by placing the source trees and MRP matrix on the World Wide Web for the scientific community to download. No shorter trees were found using this community-based method of tree-building but it still proved invaluable in the identifying of taxonomic errors that would otherwise have had a negative impact on the resultant supertree.

4.2 Introduction

Birds are an ideal candidate for supertree construction as they are of interest to vertebrate biologists and palaeontologists alike. They are diverse, with current estimates of nearly 10,000 extant species (Monroe and Sibley, 1990) occupying almost every geographical location, from ocean to desert. Birds evolved from therapod dinosaurs in the Jurassic (Chiappe, 1995 and references therein) and it is debated whether they experienced a huge burst in diversity during the Tertiary with many modern orders diversifying in a very short period of time (Feduccia, 1995) or

65 CHAPTER 4: SUPERTREE OF AVES KATIE DAVIS whether the major orders of Neornithes were already present in the Cretaceous and survived the Cretacaeous-Tertiary event (Cracraft, 1973; Cracraft, 2001; Ericson et al., 2002; Hope, 2002; Dyke, 2003; Ericson et al., 2003; Van Tuinen et al., 2003). Birds are in particular need of phylogenetic assessment as no widely accepted phylogeny currently exists that is at species level or contains both extinct and extant taxa.

Supertrees have now been produced for several groups of taxa including the Dinosauria (Pisani et al., 2002), marsupials (Cardillo et al., in 2004), bats (Jones et al., 2002), Carnivora (Bininda-Emonds et al., 1999), the Temnospondyli (Ruta et al., 2007) and all extant mammals (Bininda-Emonds et al., 2007). Supertrees can be used to address crucial questions in areas such as conservation and biodiversity studies to macroevolution (e.g. Purvis, 1995; Bininda-Emonds et al., 1999; Jones et al., 2002). Supertrees have also been constructed for some avian groups, such as the Procellariiformes (tube-nose seabirds) (Kennedy and Page, 2002) and Charadriformes (shorebirds) (Thomas et al., 2004). In addition, Barker (2002) used supertree methods to construct an avian phylogeny to look at phylogenetic diversity. However, Barker (2002) used the Sibley and Ahlquist (1990) “tapestry” as a framework, then added in lower level taxa using supertree methods for individual clades in the tree, effectively pasting together smaller phylogenies into an informal supertree. No formal supertree has yet been constructed for all of Aves. This chapter will construct a formal supertree of Aves covering both extinct and extant species.

Supertrees lend themselves well to collaborative creation, in terms of data collection, but perhaps more readily to construction of the actual supertree as computational limits are often the reason for non-completion of analysis. Although some phylogenetic software can run on so-called supercomputers, utilising multiple processors on the same problem to reduce the amount of time taken to complete an analysis, they obviously require access to such hardware to run at their full potential. The supertree data in this chapter was therefore made freely available to the scientific community in an attempt to build the supertree in a collaborative fashion, with the hopes that this would increase efficiency, correct any errors missed by the author, and decrease the time taken to find shorter trees.

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4.3 Methods

4.3.1 Data collection

As in Chapter 3, potential source trees were identified initially from online resources. The Web of Knowledge 1 Science Citation Index was searched; covering the years 1981 to 2005 and all papers potentially containing trees were examined. The reference lists within these papers were then searched for papers containing trees. All papers containing trees were retained and this process was continued until as many trees as possible were found. Papers were collected up to the end of December 2005 as at that point data processing commenced. A total of 589 papers were collected for the Aves species-level dataset that were deemed to contain potentially useful source trees, of these 30 were found to contain trees that were redundant because they a) reanalysed previous datasets and added no new data or taxa or b) did not contain an original tree. Category a) trees were dealt with according to the protocol (described fully in Chapter 3 and summarised below), while category b) source trees were discarded. While every effort was made to collect all references, there is a great wealth of information regarding avian phylogeny and it is always possible that some may have been missed.

The 589 papers yielded 1054 trees spanning 7384 taxa. After processing following the protocol described in Chapter 3, 307 trees were eliminated, leaving 747, from 556 source papers (see Appendix B), to be used to construct the supertree. These trees contained 5274 taxa. This drop in taxa numbers was due to the removal of higher taxa, vernacular names and synonyms during data processing.

Following the protocol, described in detail in Chapter 3, attempts were made to remove as much dubious data from the diverse range in input trees as possible. Briefly, the protocol aims to standardise taxonomy, remove non-independent trees, allow the combination of taxa at different levels, and accommodate paraphyletic taxa. The source trees, along with associated metadata, were first collected in their

1 http://wok.mimas.ac.uk

67 CHAPTER 4: SUPERTREE OF AVES KATIE DAVIS original form from the source papers collected. The next stage was to correct names using the Taxonomic Name Server (Page, 2005). Any names not validated using this tool were checked manually from a number of sources, including the original source (as was often the case for fossil taxa) and even Google 2 in an attempt to find the correct name (see Appendix A for a list). Any non-avian taxa (e.g. dinosaurian outgroups in fossil avian trees) were deleted before the matrix was created as “pruning a taxon from an MRP matrix will create a matrix that is not representative of the real topology of the pruned tree” (Pisani et al., 2002).

Next, non-independent studies were identified using a Perl script which allows a semi-automated method of identifying such studies and bringing them to the attention of the user. Finally paraphyletic taxa and taxa at different taxonomic levels were dealt with using a range of Perl scripts (see Chapter 3 for full details of the protocol and Appendix F).

In the test case (Chapter 3) there were only a small number of supraspecific taxa and vernacular names in the source trees (e.g. “New World Quail” and “ Alectura ” as two examples in Sibley and Ahlquist, 1990). This meant that these OTUs (operational taxonomic units) could be replaced with the relevant species by hand. In the main supertree dataset this was not feasible. For example, a number of source trees contained the taxa “Neornithes”, “Carinatae” or “modern birds”, which requires the substitution of virtually every taxon contained within the supertree. It would be impossible, and hugely error-prone, to deal with this by hand and therefore a Perl script was employed to facilitate the substitution of these, and other, higher taxa and vernacular names (Appendix F: replace_higher_taxa.pl).

At this point the trees were checked for sufficient overlap (Sanderson et al., 1998). All trees contained at least two taxa that overlapped with another source tree so all could be incorporated into the supertree analysis.

Once the data had been processed according to the protocol, the matrix was constructed using a version of Bininda-Emonds’ SuperMRP.pl Perl script (Bininda-

2 http://www.google.co.uk

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Emonds et al., 2005) that was modified to run in Windows (see Appendix E for the matrix). A Nexus-formatted tree file containing all source trees was then constructed, again with a simple Perl script. The output from this is two tree files and a text file. One of the tree files contains all trees with correct labels according to the source from which they were taken. The second tree file contains the same trees, but they are labelled sequentially from 1 to n. The text file then contains a key indicated from which source each tree is from. It is this second tree file, along with the MRP matrix, that was uploaded to the Bird Supertree project website 3. The website contained an online viewer for all trees uploaded (both source and any resulting supertrees), a ‘blog’ and information on the project. Researchers could then, independently, create a supertree using whatever methods they wished. The intention was that the person who uploaded the shortest tree would be asked to co-author a paper describing this work, while any persons finding shorter trees than that in the results section below would receive an acknowledgement.

Once all data processing was completed, the data contained 5274 taxa from 746 source trees, from 556 source references.

4.3.2 Analysis

The Galliformes supertree test study (Chapter 3) showed that TNT (Goloboff et al., 2008) was far superior at finding shorter trees in a shorter timescale than PAUP* 4.0b10 (Swofford, 2002), either when using a standard heuristic search or when implementing the Parsimony Ratchet (Nixon, 1999). Therefore the MRP matrix was analysed in TNT (Goloboff et al., 2008) using the “xmult level=10” option, an aggressive search strategy devised to find the shortest trees in as little time as possible. Although other supertree methods are available with software implementation (see Chapter 1), there are none that can handle such large numbers of taxa. Therefore it was necessary to use MRP (Matrix Representation with Parsimony) for this analysis, despite the various criticisms that the method has received (Gatesy et al., 2002; Gatesy et al., 2004; Wilkinson et al., 2005b).

3 http://linnaeus.zoology.gla.ac.uk/~rpage/birdsupertree/

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The analysis ran for 12 hours, the longest queue available on the machine used. Analyses were carried out on “Ness”, a 64 processor cluster, consisting of 2.6 GHz AMD Opteron (AMD64e) processors with 2 GB of memory per processor, hosted at EPCC, University of Edinburgh. Only a single processor was used for this study.

In addition to the above analysis, the data were made available publicly via the “Bird Supertree Project” website. To date (December 2007) a total of four trees have been uploaded. Trees uploaded used both TNT (Goloboff et al., 2008) and PAUP* 4.0b10 (Swofford, 2002), however, no information was available on the machine used to run the analysis. In itself, this was a unique experiment in the social aspect of scientific collaboration.

4.4 Results

4.4.1 The supertree

The analysis ran for 12 hours and TNT (Goloboff et al., 2008) found a single, remarkably well resolved, parsimonious tree of length 17899. This tree is displayed in full in Figure 4.1. Higher taxa have been labelled on the supertree as defined by Howard and Moore (2003). For a larger print version of the supertree see Appendix C.

It is worth mentioning that many of the groups discussed below, and this is particularly the case within the Passeriformes, are not perfectly monophyletic but where there is a clear distinction that allows the recognition of major groups and higher taxa they have been treated as such for the sake of brevity and clarity both in this description and in the accompanying diagram of the supertree (Figure 4.1).

General overview of the tree

The Mesozoic birds are at the base of the tree. The Neornithes (modern birds) are split into the Palaeognathae (tinamous and ratites) and the Neognathae (all other taxa). Both morphological and molecular data support this basal division (Cracraft, 1988; 2001; Groth and Barrowclough, 1999; Van Tuinen et al., 2000; Livezey and Zusi, 2001). The Galloanserae (Galliformes – landfowl, and Anseriformes –

70 CHAPTER 4: SUPERTREE OF AVES KATIE DAVIS waterfowl) then form a monophyletic sister group to the Neoaves (Neognathae minus Galloanserae).

Figure 4.1: Single MPT of length 17899 found by TNT (Goloboff et al., 2008). The inner ring shows orders, whilst the outer rings split the Passeriformes into more manageable sections (families and some genera) to better show areas of interest. Individual taxa are not visible, see Appendix C for a version of the tree in which all taxa can be read.

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Within Neoaves, the hoatzin has been placed at the base of a clade containing the Musophagiformes (turacos and allies), Pteroclidiformes (sand grouse) and Columbiformes (doves and pigeons). The Phoenicopteridae (flamingos), Podicipedidae (grebes), Gaviiformes (loons), Sphenisciformes (penguins), Procellariiformes (tube-nose seabirds), (totipalamate birds), Ciconiiformes (storks and allies), Turnicidae (buttonquail) and Charadriiformes (shorebirds) all form a monophyletic group as in Sibley and Ahlquist’s (1990) “Ciconiiformes”. The one exception is the Falconiformes (diurnal birds of prey) which are placed with the Strigiformes (owls), then this clade is sister taxon to the other “ciconiiform” orders. The Cuculiformes (cuckoos and anis) are placed as sister to a clade containing the Trogoniformes (trogons), (nightbirds), Aegotheliformes (owlet-nightjars) and Apodiformes (swifts and hummingbirds). The latter three have been placed together by both DNA-hybridisation data (Sibley and Ahlquist, 1990) and by cranial morphological characters (Livezey and Zusi, 2001). The Coliiformes (mousebirds) and Psittaciformes (parrots and allies) form the sister group to a clade containing the (hornbills), Coraciiformes (kingfishers and allies), Galbuliformes (puffbirds) and Piciformes (woodpeckers and allies). The affinities of the latter four to each other have been suggested by a number of workers (e.g. Espinosa de los Monteros, 2000; Johansson et al., 2001). The Passeriformes (perching birds) form a large monophyletic group that is split into two fundamental divisions; the suboscines and the oscines (songbirds). The suboscines are further split into Old World and New World taxa. The oscines can be subdivided into a paraphyletic “Corvida” ( sensu Sibley and Ahlquist, 1990), which contains two distinct clades (the honeyeaters and allies, and the corvoid birds), and the Passerida, which contains three superfamilies; the Sylvioidea, Muscicapoidea and Passeroidea. The taxa within these subfamilies are more concordant with the definition of Barker et al. (2002) than that of Sibley and Ahlquist (1990).

Lower-level relationships

The Mesozoic fossil birds are placed at the base of the tree with Archaeopteryx lithographica occupying the most basal position. Within these the Enantiornithes form a distinct monophyletic clade. The Enantiornithes are thought to represent a separate Mesozoic radiation to the Ornithurae (the direct ancestors of modern birds)

72 CHAPTER 4: SUPERTREE OF AVES KATIE DAVIS that subsequently became extinct at the Cretaceous-Tertiary boundary (Sanz and Buscalioni, 1991; Feduccia, 1995; Hou et al., 1996; Zhang et al., 2001).

Within the Neornithes the Palaeognathae are sister to the remainder of Neornithes – the Neognathae, as in the traditional classification (Stapel et al., 1984). The extinct palaeognath taxa and the monophyletic – Megalapteryx (upland moa), Dinornis (giant moa), Anomalopteryx (lesser or bush moa), Euryapteryx (stout- legged moa), Emeus (eastern moa) and Pachyornis (heavy-footed moa) – are at the base of the extant palaeognaths. These are then split into two monophyletic clades comprising the Struthioniformes (ratites) and Tinamiformes (tinamous) with the extinct “” ( Aepyornis ) at the base. The New Zealand ratites – Apterygidae (kiwis) and Dinornithidae (moa) do not form a monophyletic group, a grouping also found by Houde (1987) and Cooper et al. (1992) who suggest that this is evidence for a second colonisation of New Zealand by kiwis.

At the base of Neognathae the Galliformes (landfowl) and Anseriformes (waterfowl) form a monophyletic Galloanserae as proposed by Caspers et al. (1997), which is sister taxon to the remainder of extant birds (Neoaves) forming a monophyletic Neognathae as suggested by Cracraft (1988) and Van Tuinen et al. (2000) and in contrast to Sibley and Ahlquist’s (1990) non-monophyletic Neognathae in which the Galloanserae are sister group to the Palaeognathae. Within the Anseriformes the extinct Cnemiornis is placed as a sister taxon to the Dendrocygnidae and , as suggested by Livezey (1989; 1996). Within the Galliformes, the families and subfamilies follow the same large-scale pattern as that found in the galliform test cases of Chapter 3, i.e. (Megapodiidae, (Cracidae, (Numididae, (Odontophoridae, (Phasianidae, (Meleagridinae, (Tetraonidae))))))).

The hoatzin ( Opisthocomus hoazin ) is placed at the base of the next clade which contains the Musophagiformes (turacos and allies) and Pteroclidiformes (sand grouse) that then form the sister taxon to a monophyletic Columbiformes (doves and pigeons). Although Opisthocomus has often been placed with the Cuculiformes (cuckoos, coucals and anis) (Hughes, 2000; Johnson et al., 2000; Hedges et al., 1995) and even with the Gruiformes (crakes and rails) (Livezey and Zusi, 2001) some workers have suggested a relationship with the Musophagiformes (Hughes and Baker, 1999; Sorenson et al., 2003) so this placing is not entirely unexpected.

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Pteroclidiformes have been placed with the Columbiformes in a number of source trees (e.g. Rotthowe and Starck, 1998; Paton et al., 2003). The relationships of the Columbiformes are quite uncertain (Sibley and Ahlquist, 1990). They have been placed close to the Passeriformes (Van Dijk et al., 1999) but, as seen here, have also been placed with the Musophagiformes (Van Tuinen et al., 2000). After this a monophyletic Gruiformes is sister to a clade containing Strigiformes (owls), Falconiformes (diurnal birds of prey), Phoenicopteridae (flamingos), Podicipedidae (grebes), Gaviiformes (loons), Sphenisciformes (penguins), Procellariiformes (tube- nose seabirds), Pelecaniformes (totipalmate birds), Ciconiiformes (storks and allies) and Charadriiformes (shorebirds) (with Turnix at the base). The Turniciformes (buttonquail – Turnix ) have presented many problems in the history of avian phylogeny. Superficially they look like true quails but have traditionally been placed in the Gruiformes (Fürbringer, 1888; Sibley and Ahlquist, 1990). More recent analyses have placed them in the Ciconiiformes (Van Tuinen et al., 2000) as is seen in the supertree. These relationships are similar to Sibley and Ahlquist’s (1990) definition of “Ciconiiformes” containing the traditional orders Pelicaniformes, Procellariiformes, Charadriiformes, Falconiformes, Sphenisciformes, Podicipedidae and Gaviiformes, with the exception of the Falconiformes, which cluster with the Strigiformes as sister taxon to the main clade. Within Falconiformes are Accipitridae (Old World vultures) whilst the New World Vultures (Cathartidae) are placed close to the storks (Ciconiidae). All these clades are resolved largely as monophyletic groups (as in Storer, 1971; Griffiths, 1994; Paterson et al., 1995; Nunn, 1998; Fain and Houde, 2007). The Sphenisciformes (penguins), Gaviiformes (loons) and Podicipedidae (grebes) have been considered to be closely related by Cracraft (1985), which is the outcome of the supertree analysis. Phoenicopteridae (flamingos) have been suggested to be related to grebes (Van Tuinen et al., 2001) and in the supertree have been placed at the base of the clade containing the grebes, loons, penguins and tube-nose seabirds.

This clade is followed by a monophyletic Cuculiformes then a monophyletic Trogoniformes (trogons). The Cuculiformes is split into two clades containing the Neomorphinae (roadrunners) and Crotophaginae (anis) (Hedges et al., 1995; Johnson et al., 2000) and the Coccyzinae (New World cuckoos) and Cuculinae (Old World cuckoos) (Hedges et al., 1995; Aragon et al., 1999; Hughes, 1999; Johnson et al.,

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2000). The next clade contains a monophyletic Caprimulgiformes (nightbirds), Aegotheliformes (owlet-nightjars) and Apodiformes (swifts and hummingbirds) (contains monophyletic Apodidae and Trochilidae – which supports Sibley and Ahlquist’s (1990) suggested “Trochiliformes” for taxa). The association between the Apodiformes (swifts) and Trochiliformes (hummingbirds) has long been recognised (Bleiweiss et al., 1994; Van Tuinen et al., 2000; Johansson et al., 2001; Mayr, 2002) and is not contradicted by any of the source trees. Sibley and Ahlquist (1990) placed Caprimulgiformes within the Strigiformes (Caprimulgiformes was split and renamed Caprimulgi and Aegotheli), however, here the Caprimulgiformes are not placed in even the same clade as the Strigiformes (described earlier).

Next, the Coliiformes (mousebirds) form the sister taxon to a monophyletic Psittaciiformes (parrots and allies). Espinosa de los Monteros (2000) has suggested this relationship for the Psittaciformes, which are traditionally considered to have no close living relatives (Sibley and Ahlquist, 1990). These are sister to a clade containing the monophyletic Coraciiformes (kingfishers and allies), Galbuliformes (puffbirds) and Bucerotiformes (hornbills), which form a monphyletic sister group to the Piciformes (woodpeckers and allies). The Hoopoe, Upupa epops , is placed within the Coraciiformes in contrast to Sibley and Ahlquist’s (1990) suggestion of a new order “Upupiformes”. The Piciformes are split into two distinct clades, one containing the Ramphastidae () and the Capitonidae (New World barbets) (Simpson and Cracraft, 1981; Swiersczewski and Raikow, 1981; Lanyon and Zink, 1987; Lanyon and Hall, 1994) and the second containing the Picidae (woodpeckers) and the Indicatoridae () (Simpson and Cracraft, 1981; Swiersczewski and Raikow, 1981; Lanyon and Zink, 1987). This clade forms the sister group to a monophyletic Passeriformes (perching birds), which are placed in a derived position within the tree in agreement with traditional views on the timing of their divergence relative to other orders (Johansson et al., 2001). The Passeriformes are the perching birds and contain more than half of all extant avian species.

Acanthisitta and Xenicus (New Zealand wrens) are at the base of the Passeriformes. The remainder of the Passeriformes are split into monophyletic suboscines and oscines (songbirds). This is the traditional view of phylogeny and is

75 CHAPTER 4: SUPERTREE OF AVES KATIE DAVIS supported by many previous analyses (e.g. Christidis et al., 1996; Edwards et al., 1997).

The suboscines are split into monophyletic Old World and New World groups. The Old World suboscines contain the Philepittidae (Asities), Eurylaimidae (broadbills) and Pittidae (pittas) and Sapayoa, which is at the base of the Eurylaimidae. Sapayoa aenigma is found in Panama and northwest South America and was traditionally placed in the New World suboscines, although it has more recently been placed in the Old World suboscines in varying positions (Prum, 1990; Fjeldsa et al., 2003; Chesser, 2004a). Monophyly of the Old and New World suboscines is well- documented (e.g. Irestedt et al., 2001; Irestedt et al., 2002).

The New World suboscines are further split into two monophyletic groups; the tracheophone suboscines (Furnariidae – ovenbirds, Conopophagidae – gnat-eaters, – ground antbirds, Rhinocryptidae – tapaculos, Thamnophilidae – antbirds and Dendrocolaptidae - woodcreepers) and the non-tracheophone suboscines (Tyrannidae – tyrant-flycatchers, Pipridae – and Cotingidae - cotingas).

The Pipridae and Cotingidae both form monophyletic groups. The vast majority of the Tyrannidae are found in a single monophyletic group, some however are placed at the base of the non-tracheophone suboscines and at the base of the suboscine/oscine clade. Within the remainder of the tracheophone suboscines, the Thamnophilidae and Rhinocryptidae are resolved as a monophyletic group, but the remainder of the families are paraphyletic.

The oscines, or songbirds, comprise the majority of the Passeriformes. Their relationships are poorly understood and are the subject of much confusion and controversy, a fact that probably explains the chaos and untidiness that characterises this portion of the supertree.

The Menuridae (lyrebirds) and Atrichornithidae (scrub-birds) have been placed at the base of Passeriformes in the supertree (as in Sibley and Ahlquist, 1990; Ericson et al., 2002). These, with a monophyletic Climacteridae (treecreepers) and Ptilonorhynchidae (bowerbirds), form the sister group to the remainder of the oscines. This is a relationship supported by a number of workers (Sibley and

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Ahlquist, 1990; Christidis et al., 1996; Ericson et al., 2002), although many analyses have widely separated these taxa with the bowerbirds placed close to the birds of paradise (Paradisaeidae) (Espinosa de los Monteros and Cracraft, 1997; Cibois and Pasquet, 1999) and also with the babblers (Timaliidae) (Edwards and Arctander, 1997).

The next portion of the tree comprises a number of large clades that correspond to Sibley and Ahlquist’s (1990) “Corvida”, although they form a paraphyletic group with the “Passerida” nested within. This part of the tree is split into two clades that correspond to the two main assemblages in Christidis and Schodde’s (1991) Australo-Papuan songbirds. The first clade (honeyeaters and allies) contains the Irenidae (fairy ) which, with the Chloropsidae (leafbirds), form the sister taxon to a group containing the Maluridae (“wrens”), Meliphagidae (honeyeaters), Acanthizidae (Australian warblers) and Pardalotidae (), in a larger clade with the Orthonychidae (logrunners) and Pomatostomidae (Australasian babblers). The Meliphagidae are monophyletic but the Acanthizidae and Pardalotidae are paraphyletic. The second clade contains the corvoid birds including the Melanocharitidae (berrypickers and longbills), Vireonidae (vireos), Pachycephalidae (whistlers and allies), Oriolidae (orioles), Campephagidae (-shrike and allies), Artamidae (woodswallows), Malaconotidae (bushshrikes), Platysteiridae (wattle- eyes), Vangidae (vangas), Dicruridae (drongos), Monarchidae (monarchs), Paradisaeidae (birds of paradise), Laniidae (shrikes), Corvidae (crows and allies) and Petroicidae (Australian robins). Not all of these form perfectly monophyletic groups but they do all form well-defined clear clades. These two clades are thought to represent two endemic radiations (Christidis and Schodde, 1991).

The remainder of the passeriform birds represent the Eurasian radiation and correspond to Sibley and Ahlquist’s (1990) “Passerida”. Unlike the “Corvida” these form a monophyletic group.

The clade containing the Paridae (tits), Alaudidae (larks) and Hirundinidae (swallows) forming a sister to the Pycnonotidae (), Cisticolidae (cisticolas and allies), Sylviidae (Old World warblers), Timaliidae (babblers) and Zosteropidae (white-eyes) corresponds to the superfamily Sylvioidea. First suggested by Sibley and Ahlquist (1990), the results shown here correspond more closely with the

77 CHAPTER 4: SUPERTREE OF AVES KATIE DAVIS definition of Barker et al. (2002). It is important to note that although the large-scale relationships fit well with expectations, within these higher taxa the families, and even genera, are quite poorly defined and rarely form monophyletic groups.

Another clade containing the Regulidae (kinglets), Sittidae (nuthatches), Certhidae (treecreepers), Polioptilidae (gnatcatchers), Troglodytidae (wrens), Mimidae (mimids), Sturnidae (), Turdidae (thrushes) and Muscicapidae (Old World flycatchers) represents the superfamily Muscicapoidea. Again, these families are not necessarily monophyletic.

The next clade contains the Promeropidae (sugarbirds), Dicaeidae (flower-peckers), Nectariniidae (sunbirds), Prunellidae (accentors), Estrilididae (Estrilid finches), Ploceidae (weavers), Passeridae (Old World sparrows), Motacillidae () and the nine-primaried oscines. Many of these families are paraphyletic and this part of the tree is quite untidy and unclear. This clade does, however, correspond to the third superfamily, Passeroidea, again as defined by Barker et al. (2002).

Within the Passeroidea, the nine-primaried oscines, which contain approximately 10% of all extant species of bird (Klicka et al., 2000), form a monophyletic clade. This contains a monophyletic Fringillidae (finches), Cardinalidae (cardinals) and Parulidae (New World warblers) then another monophyletic clade containing a paraphyletic Icteridae (blackbirds and allies), Emberizidae (American sparrows, buntings and allies) and Thraupidae (). The Coerebidae (bananaquits) are placed within the non-monophyletic Emberizidae and Thraupidae.

4.4.2 Novel clades

There were some novel clades present in the tree. An observation was that all those taxa examined were either a) only present in a small number (often only one) of source trees as part of a polytomy, or b) the taxa were in well-resolved positions in a single source tree and there was no obvious reason for MRP placing them in these spurious groups. Not all will be discussed here but a number have been considered below.

Those taxa whose positions can be explained by a lack of taxonomic constraint include: Bombycilla japonica which is placed within the Maluridae with the fossil

78 CHAPTER 4: SUPERTREE OF AVES KATIE DAVIS taxon NHMM/RD 271. This is only found in one source tree (Pasquet et al., 1999) in a polytomy. A large number of poorly-placed taxa are in a large polytomy at the base of the Passeriformes next to Acanthisitta and Xenicus . These are all passeriform birds (plus the fossil roller, Geranopterus alatus ) and there is no logical basis for the positioning of these taxa. The following taxa are all part of this clade and each appear in only a single source tree and as part of polytomies: Myiagra ferrocyanea (steel-blue flycatcher) – in Filardi and Smith (2005); Pteruthius xanthochlorus (green shrike-babbler) and Pteruthius rufiventer – (black-headed shrike-babbler) – in Cibois (2003); Andropadus curvirostris (plain ) and Andropadus importunus () – in Roy (1997).

Many of the novel clades were as a result of poorly constrained fossil taxa. Eocoracias (a middle Eocene roller) is placed with Palaeotis (a basal ratite) at the base of the Palaeognathae. This is a logical positioning for Palaeotis but there is no reason for Eocoracias to be placed here. It occurs in two source trees, one as sister to all other taxa (Mayr and Mourer-Chauvire, 2000) and in the other as part of a large polytomy (Mayr et al., 2004). The Mesitornithidae ( Mesitornis and Monias ) are thought to be related to the cuckoos (Cuculiformes) (Mayr and Ericson, 2004) but have been placed within the Caprimulgiformes with Steatornis () and the extinct oilbird taxon – Prefica nivea . The Quercypsittidae, which comprises two species of fossil , is placed at the base of the clade containing the Coliiformes and Psittaciformes. Pulchrapollia gracilis , another fossil parrot, has been placed within the Coraciiformes. Geranopterus alatus , a fossil roller (Coraciiformes), is placed at the base of the Passeriformes with the New Zealand wrens. Another fossil roller of the same genus, Geranopterus milneedwardsi, has been placed within the Maluridae (Passeriformes). Finally, the unassigned fossil taxon NHMM/RD 271 was also placed within the Maluridae. Many of these fossil taxa are only represented in a single source tree and often only as part of a polytomy, for example, the fossil taxon NHMM/RD 271 is only found in Dyke et al. (2002) in a polytomy with Anas and .

Less easy to explain are those that appear in well-resolved positions in source trees. Some examples are Telophorus bocagei (bushshrike) – in Smith et al. (1991); and

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Catharus fuscater (slaty-backed nightingale-) and Catharus mexicanus (black- headed nightingale-thrush) – both in Outlaw et al. (2003).

4.4.3 Results of the “community tree-building” approach

The community aspect of this project produced a total of four result trees at the time of writing (December 2007). Two of them were uploaded by the author. The trees uploaded by other interested parties were produced using TNT. Both were longer than the tree presented here and therefore have not been shown. Although not many trees were uploaded a number of errors, both taxonomic and syntactical, were identified in the source data by viewers of the uploaded source trees and, in this way, the community approach did greatly improve the quality of the supertree. As an example, the original uploaded source data was found to contain four duplicated albatross taxa, in the form of synonyms, which needed to be removed before any further analyses were carried out.

4.5 Discussion

The results show that the supertree is a reasonable assessment of the current understanding of avian phylogeny. As with the Galliformes supertree in Chapter 3 though, it would be advisable, at present, to view it only as an assessment rather than as a definitive statement of avian phylogeny and evolution. There are a number of novel clades, but these all occur at lower taxonomic levels and it is clear that the majority of these have arisen as a result of poor taxonomic sampling.

Many of the novel clades and poorly placed taxa are a result of low taxon sampling. This statement is made more robust as the protocol used to build the supertree ensured consistent naming of taxa, which may have exacerbated this problem. The protocol and data storage mechanisms (see Chapter 3) also made it very easy to pinpoint which sources trees contained taxa in novel clades and other spurious groupings. While novel clades are essentially an undesirable result, they are useful in that they pinpoint areas of phylogeny that need more research, which is, in fact, one of the justifications for supertrees in that they can highlight areas of poor taxonomic sampling (Bininda-Emonds et al., 2002).

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However, there were some taxa for which there was no obvious reason for their spurious placement in the tree. It is possible that this is an undesirable property of MRP (Matrix Representation with Parsimony). It is also possible that given more time to run the analysis (there was a queue length limit of 12 hours on the machine used) these anomalies would be resolved. Running the supertree on a similar machine for an increased length of time is an obvious next step to take in investigating these results as it is possible that further analysis of the data may find shorter trees. This could be surprisingly successful as the tree presented here was only four steps shorter than the second shortest tree found and yet was successful in resolving the positions of a number of the fossil taxa which had been placed in obviously spurious clades in the second shortest tree.

No measures of fit were added as there are currently none appropriate for supertrees in existence. Ruta et al. (2003) state that “statistical methods devised to assess branch support in character-based trees are problematic for supertrees”. Bininda- Emonds (2003) developed QS values, Qualitative Support, and applied them to a supertree of marsupials (Cardillo et al., 2004). The QS index works by comparing source trees with the supertree and assigning one of four “states” for the fit between the two. A hard match occurs where the source tree fits the supertree exactly, a soft match occurs where addition of missing taxa may support the clade but never contradict it and vice versa for a soft mismatch, finally, a hard mismatch occurs where the source tree contradicts the supertree. However Wilkinson et al. (2005a) state that the QS values are flawed as the categories defined by Bininda-Emonds (2003) were not mutually exclusive, for example the definitions of equivocal and soft support both contain no hard matches or mismatches and both contain soft mismatches.

The community aspect of the project was not very successful. Although a few data problems were found by others (taxon duplication and a few erroneous trees) only one other person had uploaded a final tree at the time of writing. However, this approach did pick out problems such as duplicate taxa () and empty leaves, which were a result of a syntactical error in the taxa substitution script. These problems were subsequently dealt with before re-running the matrix. It is surprising

81 CHAPTER 4: SUPERTREE OF AVES KATIE DAVIS that the project did not attract more attention as a large species-level supertree is very much in demand at the present time.

4.6 Conclusions

This study has produced the largest, to the author’s knowledge, supertree of both extinct and extant avian species using robust data collection and processing methods. The tree contains over half of the known extant avian fauna. Over 5000 individual species or genera were included, covering 24 years worth of systematic research into Aves, and five times as inclusive as the next largest study, Sibley and Ahlquist’s “tapestry” (1990). This level of taxonomic coverage would simply not have been possible with any other method of constructing large-scale phylogenies.

The results were sensible, giving a reasonable summary of the current knowledge of avian phylogeny. It is clear though that there is still much work to be done and there are a number of areas that require much more primary data collection and analysis. Many of these areas were identified by the presence of novel clades, which, on inspection, were evidently the result of poor taxonomic sampling. Other novel clades were as a result of the inclusion of fossil taxa, the only solution here is for more fossils to be described and included in phylogenetic analyses. Finally, there were some spurious groups that can not be easily explained. These could be due to undesirable properties of MRP or may be resolved simply be further analysis, as the current analysis was, by necessity, limited to a run time of just 12 hours.

The tree presented here is the largest species-level supertree constructed, to the author’s knowledge, and will provide a useful resource for researchers studying avian macroevolution, biodiversity and character evolution. One such study would be to date the tree as in Bininda-Emonds et al. (2007) mammal supertree. This could be particularly interesting as the avian supertree presented here has incorporated fossils, something not covered by Bininda-Emonds (2007). In addition, the tree provides a “straw man” for further systematic research into Aves.

The next chapter takes a look at the supertree versus supermatrix “controversy” and builds two Galliformes phylogenies in order to compare and contrast the two methods.

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Chapter 5

Supermatrix or Supertree? A comparison of supertree and supermatrix methods

5.1 Abstract

There are two distinct methods available to construct large-scale trees: supermatrix and supertree. Each has advantages and disadvantages, but supertrees in particular have come under heavy criticism from some authors. Supertrees are secondary constructions, built from individual phylogenetic trees, whereas a supermatrix is constructed from primary data collated into a single, large matrix. This chapter looks at the supertree vs. supermatrix “controversy” in order to assess which, if either, is a more suitable method of building large phylogenetic trees. A molecular-only tree was constructed using both methods, using the same data, thus ensuring that neither method had an advantage. Each output tree was then compared to the input source trees of the supertree as a method of assessing how each large-scale phylogeny represented the smaller, independent, source studies. Both methods performed equally as well in fitting the source data. The supermatrix was much quicker to construct, but took substantially longer to calculate. The supertree took a long time to construct, mainly due to the stringent data control protocols in place (see Chapter 3), but was very quick to calculate. Dependent upon the data at hand and the other factors involved, the choice of which method to use appears, from this small study, to be of little consequence.

5.2 Introduction

Supertree and supermatrix methods are two general approaches used to construct large trees from datasets with a diverse array of data. Supertrees have been discussed fully in previous chapters, however some workers believe that supertree methods cannot add anything to our knowledge of the tree of life and that supermatrices should instead be constructed (Gatesy et al. , 2002; Gatesy et al. , 2004; Queiroz and

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Gatesy, 2006). A supermatrix represents the total evidence approach, where characters and taxa make up a single large matrix and the data are analysed simultaneously (Miyamoto, 1985; Kluge, 1989; Nixon and Carpenter, 1996).

Gatesy et al. (2002) argue that supertrees “are imprecise summaries of previous work” and that a supertree cannot be a better depiction of previous research (referring to Purvis, 1995; Bininda-Emonds et al. , 1999; Liu et al. , 2001; Jones et al. , 2002) than a supermatrix, due to the fact that supermatrices clearly review which characters have or have not been scored for particular taxa. These primary data are presented with no duplications or editing errors, and are easily accessible for examination by other researchers. In contrast, Queiroz and Gatesy (2006) state that in supertree analyses some of the character information is lost when sets of characters are combined as trees. The finding that trees produced by supermatrix analyses tend to be better resolved than those from supertree analyses is also thought “to reflect the greater information content of supermatrices and the associated emergence of hidden support” (Queiroz and Gatesy, 2006).

With regards to hidden support it is suggested that while supermatrices can produce novel clades as a result of hidden character support with a well-characterised basis (Barrett et al. , 1991; Gatesy et al. , 1999; Lee and Huggal, 2003), Matrix Representation with Parsimony (MRP), by far the most commonly utilised method of supertree construction, ignores or misinterprets hidden character support in different source data sets and produces novel clades with no logical basis (Gatesy et al. , 2004).

Simulations have shown that MRP can approximate total evidence (Bininda-Emonds and Sanderson, 2001). Gatesy et al. (2004) however, state that these simulations are run on ideal data and that none of these conditions are duplicated in published MRP supertree datasets. Therefore, they believe that these simulated results cannot be taken at face value.

A drawback of the supermatrix approach is that some types of data, such as from DNA-hybridisation and immunological distances, cannot be combined into a single data matrix (Sanderson et al. , 1998). However, Gatesy and Springer (2004) believe that the types of information that cannot be included in a supermatrix are limited to

84 CHAPTER 5: GALLIFORMES SUPERMATRIX KATIE DAVIS those which are partially redundant, obsolete, or have no clear empirical basis, and as such is “not a great loss of taxonomic information”.

The other issue with supermatrix analyses is that as more genes and characters are added and the datasets become ever larger, there are only a few taxa in common between datasets and as such, most of the data matrix will be scored as question marks, which requires a huge input of collective effort and time to fill in these gaps (Sanderson et al. , 1998). Therefore, the included taxa must be limited in order to avoid these problems, which results in supermatrices often offering much poorer taxonomic coverage than that possible from a supertree analysis. Figure 5.1 shows an example of a data availability matrix for green plants, showing that only a small number of genes (horizontal axis) have been sampled for a large number of taxa (vertical axis) and vice versa.

Figure 5.1: Data availability matrix for green plant proteins from GenBank (release 132). The figure shows that there are a large number of genes sampled for only a few taxa and many taxa sampled for just a few genes. Each dot represents a single gene sampled for a single taxon. Species were ordered according to the number of genes sampled, with better sampled species at the top. Similarly, the more commonly used genes are to the right, so the top right corner contains the densest concentration of data. The rest of the matrix is sparsely covered. From Sanderson and Driskell (2003).

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As a response to these statements, Bininda-Emonds (2004) states the belief that supertrees and supermatrices analyse different data using different assumptions and methods, and therefore should be seen as complementary, not competing. Thus when these different approaches produce the same results there should be an increased level of confidence in those results. Where they disagree, this should indicate a need for further investigation.

Some previous studies have carried out some comparisons of supermatrix and supertree results. For example, Gatesy et al. (2002) looked at the percentage of shared key nodes and Price et al. (2005) considered clade congruence between the trees. The key difference with this work is that both these previous studies only considered how similar the trees were to each other rather than how well they represented the source data.

To investigate these issues, two trees for Galliformes will be compared. One will be created from a supermatrix and one from a supertree analysis constructed from source trees derived from the same data used to construct the supermatrix. The trees will also contain the same taxa. The aim is to determine which method, if either, produces results more consistent with the source data for the supertree. Galliformes were chosen as they are a well-known group with well-documented monophyly. Also, this group was used in Chapter 3 to test the supertree protocol so this provides a good opportunity to compare and contrast methods of creating large phylogenetic trees on a pre-existing dataset. It was decided that a molecular-only study would be carried out as this information is easy to collate from the pre-existing data collected for the supertree and from online sources, such as GenBank 1 for the supermatrix. The original Galliformes dataset from Chapter 3 was modified such that a molecular- only supertree (i.e. containing source trees derived from molecular only studies) analysis could be carried out. Only the data readily available for inclusion in a supermatrix analysis were retained for analysis in the molecular supertree so that an equivalent supermatrix analysis could be carried out. The trees were assessed against the input source data by using ent (Page, pers comm) (as in Chapter 3) to compare

1 http://www.ncbi.nlm.nih.gov/Genbank/index.html

86 CHAPTER 5: GALLIFORMES SUPERMATRIX KATIE DAVIS each tree to the set of input data to assess which, if either, is more consistent with the source data.

5.3 Methods

5.3.1 Data collection

Sequences for Galliformes were obtained from GenBank using a Perl script. Given a list of all Galliformes nucleotide accession numbers available in GenBank on the 2 nd September 2005, the script retrieved each sequence record in XML format using NCBI's Entrez Utilities service. The sequences were then stored in a MySQL database. Because the same gene may have multiple names, and different names may be used by different research groups when depositing their data, the database was manually edited to link gene name synonyms together. Sequences from the same genes were exported as FASTA format files for alignment.

Data for the supertree were taken from the Galliformes supertree dataset (Chapter 3). In order to make a fair comparison of methods this dataset was pruned to only contain source trees that were constructed using the same genes as those included in the supermatrix analysis. Due to the data collection methods employed, this was easy to carry out as the XML files already created for the supertree data contained all the necessary information.

After initial source tree pruning there remained a total of 30 source trees from 22 publications. The supertree dataset contained 153 taxa in the supertree dataset. The supermatrix data contained 151 taxa (152 with the outgroup Aythya ), including a number of subspecies, which obviously were not present in the supertree dataset. The supertree dataset contained 9 taxa not present in the supermatrix data. After standardisation to remove taxa not present in both datasets, 144 taxa remained.

The taxa for the supertree were checked in the Glasgow Taxonomic Name Server 2 (Page, 2005) and any synonyms were corrected. This did not result in a change of

2 http://darwin.zoology.gla.ac.uk/~rpage/MyToL/www/index.php

87 CHAPTER 5: GALLIFORMES SUPERMATRIX KATIE DAVIS taxa number therefore the data processing and analysis could proceed without any further modifications to the taxa.

5.3.2 Data processing

For the supermatrix, alignments were created in ClustalX 1.83 (Thompson et al., 1997) using the default settings. The 16S rRNA alignment was trimmed and some taxa were removed from the CO1, COIII and tRNA-Trp sequences.

Supermatrix construction was automated using a Perl script. As when automating data processing elsewhere, this greatly reduced potential error and computational time. The taxon Aythya americana (redhead ) was assigned as the outgroup. Within the matrix the data were organised into 41 character-based sets.

The supertree data had already been collated for the analysis described in Chapter 3 and were processed as described in the Chapter 3 protocol. The taxonomy had already been standardised for that analysis therefore it was only necessary to remove any source trees not based on molecular data included in the supermatrix. It was then possible to proceed as usual from the “check overlap” stage (see Chapter 3). This check showed that four trees were now no longer connected to the main cluster (Figure 5.2), therefore these were pruned from the dataset in order to fulfil the requirement of all trees overlapping by a minimum of two taxa with at least one other tree (Sanderson et al., 1998). Once these trees were removed from the dataset the overlap was recalculated and it was found that all trees were now connected by the minimum required number of taxa (see Figure 5.3). Running a supertree analysis with these four pruned trees included produced obviously anomalous results. After carrying out this additional pruning of source trees the taxa number needed to be adjusted again and therefore the final trees contained 119 taxa. After all modifications to the included taxa, the final dataset contained 59% of the taxa included in the Galliformes supertrees of Chapter 3. See Appendix E for the final list of source trees.

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Figure 5.2: Graphical representation of minimal overlap of source trees after pruning of non-molecular source trees. The island consisting of four source trees needs to be removed from the study.

Figure 5.3: Graphical representation of minimum overlap after pruning of the four disconnected trees in Figure 5.2.

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After a final check of the data integrity to ensure that no errors had been introduced, the MRP (Matrix Representation with Parsimony) matrix was created, first by combining the source trees into a single file (Appendix C), then the matrix was created using a version of Bininda-Emonds’ SuperMRP.pl Perl script (Bininda- Emonds et al., 2005) which had been modified to run in Windows.

5.3.3 Analysis

The supermatrix was analysed in PAUP* 4.0b10 (Swofford, 2002) using a heuristic search, with all characters unordered, equal weighting of transformations, indels treated as missing as data, 100 random taxon addition replicates, and tree bisection- reconnection branch swapping. An attempt was made to run the matrix in TNT (Goloboff et al., 2008) as this has previously been found to find significantly shorter trees (see Chapter 3). Unfortunately it was not straightforward to reformat the matrix into a suitable format and therefore running the matrix in TNT was beyond the scope of this study due to time constraints. It seems unlikely though that this would have affected the results to a significant degree.

The supertree was analysed in both PAUP* 4.0b10 (Swofford, 2002) using the Parsimony Ratchet (Nixon, 1999) and in TNT (Goloboff et al., 2008) using the “xmult=level 10” command; an aggressive search designed to find the shortest trees.

Searches were carried out on an Apple MacBook 2.0GHz Intel Core 2 Duo with 2GB of RAM.

The resulting trees from the supertree analysis and supermatrix analysis were compared to the source trees in order to assess fit and therefore which, if either provided results more consistent with the source studies. The program ent (Page, pers comm) was used for this. Ent compares the output (from the supertree or the result of the supermatrix analysis) to all the input trees (the source trees of the supertree analysis) and gives scores for each input tree (scores are between 0 and 1 with 0 being a complete mismatch and 1 being a perfect match). This was done for both the supermatrix tree and the supertree using the source trees for the supertree as input trees.

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5.4 Results

In the supertree analysis PAUP* (Swofford, 2002) found 499 shortest trees of length 447 whilst TNT (Goloboff et al., 2008) found 12 shortest trees of length 426. The strict consensus was poorly-resolved but the 50% majority rule consensus was reasonably well-resolved and is shown in Figure 5.4.

In the supermatrix analysis a total of 20400 most parsimonious trees (MPTs) of length 41225 were found. Both the strict consensus and 50% majority-rule consensus trees were well-resolved. The 50% majority-rule consensus is shown in Figure 5.5. See Figure 5.6 for a graph of the supermatrix tree showing gene coverage per taxon.

The two trees are broadly similar and show essentially the same higher-level relationships. Figure 5.7 depicts a tanglegram showing similarities and differences between the two trees. Both are concordant with generally accepted views of galliform phylogeny. The families are not all monophyletic but do broadly fall into the pattern of (Megapodiidae, (Cracidae, (Numididae, (Odontophoridae, (Phasianidae, (Meleagridinae, Tetraonidae)))))).

The Megapodiidae and Cracidae are resolved as monophyletic groups in the trees. These taxa do not, however, form the monophyletic taxon Craciformes as proposed by Sibley and Ahlquist (1990). Instead, the results support the more traditional view of the Megapodiidae forming the sister group to all other extant Galliformes (in agreement with Dimcheff et al., 2002; Dyke et al., 2003; Gulas-Wroblewski and Wroblewski, 2003; Smith et al., 2005). A monophyletic Odontophoridae and the monospecific (in this study) Numididae are sister taxa to a monophyletic Phasianidae, which contains the majority of the galliform species.

The Phasianidae is a large order and is easier to consider as subfamilies. Subfamilies have been defined according to Howard and Moore (2003) in keeping with the definitions set for higher taxa within Chapter 3. Using this classification, the Phasianidae contains a paraphyletic Perdicinae (Old World partridges) and Phasianinae (pheasants). As already noted in Chapter 3, pheasants and partridges were originally thought to represent monophyletic lineages (Johnsgard, 1986, 1988; Sibley and Ahlquist, 1990), however, more recent evidence (Kimball et al., 1999; Geffen and Yom-Tov 2001; Smith et al., 2005) suggests that this is not actually the

91 CHAPTER 5: GALLIFORMES SUPERMATRIX KATIE DAVIS case. Both analyses produced results that are concordant with the non-monophyletic viewpoint. Within the Perdicinae the francolins are split into the quail francolins and partridge francolins as suggested by Crowe et al. (1992) and Bloomer and Crowe (1998) but are not monophyletic (in agreement with Bloomer and Crowe, 1998). The partridge francolins form a sister group to the Coturnix quails, Madagascar partridge (Margaroperdix madagarensis ) and to the Alectoris partridges, again as in Bloomer and Crowe (1998). The Phasianinae are roughly split into two groups: a group containing the peafowls and allies, and junglefowl; and a group containing the gallopheasants and allies, and the tragopans. The former group is paraphyletic in the supertree and part of a polytomy with the quail francolins in the supermatrix tree.

Meleagris , the only member of the Meleagridinae (turkeys) in this analysis, and Tetraonidae (New World quail) are each other’s closest relatives and cluster with the branch of the Phasianinae containing the gallopheasants and tragopans (as in Geffen and Yom-Tov, 2001; Dimcheff et al., 2002). Kimball et al. (1999) support the clustering of the Meleagridinae and Tetraonidae but are not able to resolve the relationship of these to other Phasianidae. In the supermatrix analysis (Perdicinae) and Pucrasia (Phasianinae) are sister taxa to the Meleagridinae and together these form the sister group to the Tetraonidae.

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Figure 5.4: Galliformes molecular supertree – shown is the 50% majority- rule consensus of 12 MPTs of length 426 found in TNT (Goloboff et al., 2008).

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Figure 5.5: Galliformes tree from the supermatrix analysis - shown is the 50% majority-rule consensus of 20400 MPTs of length 41225 found in PAUP* 4.0b10 (Swofford, 2002).

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Figure 5.6: Graph of gene coverage for the Galliformes supermatrix. Red circles indicate characters sampled for each taxon, the shaded box shows missing data.

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Figure 5.7: Tanglegram showing similarities and differences between the Galliformes supertree and supermatrix. Lines are drawn between corresponding taxa on each tree therefore the less lines that are crossed indicates higher similarity between the trees. Colours indicate families/subfamilies and are coded as in Figures 5.4, 5.5 and 5.6

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Comparisons were made between the resulting trees and the set of source trees to assess the ability of each method to accurately represent the source trees. As the data do not follow a Gaussian distribution (this is desirable as the optimum fit would be all trees with a score of 1 and hence give a non-Gaussian distribution), a non- parametric test must be used to ascertain if the difference between the weighted and combined fit scores are statistically significant. Therefore, the Mann-Whitney-U test was used to test if the difference between the means of the two samples was statistically significant.

The results show that for the supertree the mean fit scores are 0.9071 for triplet fit and 0.7227 for MASTd (higher score indicates better fit). For the supermatrix the mean fit scores are 0.8976 for triplet fit and 0.7185 for MASTd (see Table 5.1) for full statistics). Interestingly, these are much higher than the equivalent results from Chapter 3. This could be as a result of “molecular vs. morphological” conflict being removed in the molecular only dataset. The two sets of trees do still show essentially the same higher level relationships, which suggests that the molecular/morphological conflict is within the shallower nodes, i.e. species-level.

From these scores (Table 1) and the box plots (Figure 5.8) the supertree and supermatrix appear to be equivalent representations of the source data. To test this, the Mann-Whitney-U test was used, which showed that the there is no statistically significant difference between the mean fit for the supertree and for the supermatrix to a 0.99 confidence level. The calculated P-value of 0.8824 is not at all statistically significant; and shows that there is no significant difference between the means of the two samples. The majority-rule consensus trees for each method were used to generate these results.

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Table 5.1: Statistical data for “fit” scores for both the supertree and supermatrix.

Method Min 1st Qu Median Mean 3rd Qu Max.

Supertree Triplets 0.5760 0.8587 0.9205 0.9071 0.9990 1.0000

Supermatrix Triplets 0.6060 0.8407 0.9335 0.8976 0.9763 1.0000

Supertree MASTd 0.3680 0.6478 0.7140 0.7227 0.8330 1.0000

Supermatrix MASTtd 0.4000 0.6440 0.7530 0.7185 0.8397 1.0000

MASTd Fit Triplet Fit

1 1 0.9 0.9 0.8 0.8 0.7 0.7

0.6 0.6 0.5 0.5

Fit Score Fit 0.4 Score Fit 0.4 Fit score Fit 0.3 score Fit 0.3 0.2 0.2 0.1 0.1 0 0 Supertree Supermatrix Supertree Supermatrix n = 30 n = 30 n = 30 n = 30

Figure 5.8: Box and whisker plots for the supertree and supermatrix (see Table 1 for individual figures).

In addition to this, the time taken for each tree to compute was recorded (see Table 5.2). The supertree took much less time to compute in both PAUP* (Swofford, 2002) and in TNT (Goloboff et al., 2008) than the supermatrix analysis, with the TNT analysis completing in just 0.03% of the time taken by the PAUP* analysis.

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Table 5.2: Run times for computation of both trees in two different programs.

Paup TNT

Supertree 24 min 15.18 secs 35 secs

Supermatrix 36 hrs 42 min 2secs ----

5.5 Discussion

Both trees gave reasonable, sensible results with no novel clades. There were no surprises in the results and both conformed well with currently accepted views on galliform phylogeny. The trees were based on equivalent data and it is therefore reasonable to compare both with the source trees used in the supertree analysis.

There was no statistically significant difference between supertree and supermatrix tree construction methods to a 0.99 confidence level. Two scoring methods were used in order to provide a more robust test. These scoring methods are independent of each other and still gave the same result. This increases confidence in the result that each method produces results as consistent with the source data as the other.

Although both methods were equally successful at representing the source data it was far easier to create the supermatrix analysis. From initial data collection to creating the matrix, both of which can be (and were) automated, the process was much quicker than creating a supertree analysis. A supertree analysis has the potential to be computationally much faster, however, in order to ensure data quality and integrity a strict protocol (as described in Chapter 3) must be followed and this is what lengthens the whole process by a considerable amount. Conversely though, the actual run time of the supertree analysis is far quicker than that taken by the supermatrix analysis. If the supermatrix was to be rerun using TNT (Goloboff et al., 2008) it would quite probably find shorter tree in a shorter time, as found in the supertree analyses both here and in Chapter 3. However, it seems unlikely that it would complete in anywhere near as short a time as the 35 seconds taken by TNT to complete the molecular supertree analysis.

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Given the above results it seems reasonable to suggest that, in this case at least, the supertree gives as valid results as does the supermatrix analysis. One difference to note is that the supertree was significantly less well-resolved in the strict consensus than the strict consensus of the trees found by the supermatrix analysis. It seems likely that this is due to conflict between the source trees that the supertree was unable to resolve and that, therefore, if resolution is a high priority it may be worthwhile constructing a tree using supermatrix methods, whilst bearing in mind the caveats of taxonomic limitations and increased computational time.

In this study the supertree and supermatrix are identical in terms of taxonomic coverage. This was intentional in order to provide a fairer comparison. In a “real- life” scenario it would be desirable to cover as many taxa as possible and in this case it is likely that the supermatrix would not be as taxonomically complete as a supertree.

5.6 Conclusions

The aim of this chapter was to compare and contrast supertree and supermatrix methods of tree-building in light of the controversies and discussion following these techniques for creating large phylogenetic trees (e.g. in Gatesy et al., 2002; Bininda- Emonds et al., 2003; Bininda-Emonds, 2004; Gatesy et al., 2004; Queiroz and Gatesy, 2006).

The results were analysed in the same way as the Galliformes supertrees in Chapter 3 and show that there is no statistically significant difference between the tree constructed from a supermatrix and that constructed from a supertree analysis, i.e. each represents the input source data as well as the other. In this way, the two methods are complementary as suggested by Bininda-Emonds (2004), so it seems reasonable that these are good representations of galliform phylogeny.

Both trees were very similar in terms of large-scale relationships. Each gave sensible results and no spurious groups were identified. The higher-level relationships did not differ to those found in the taxonomically more inclusive Galliformes supertrees constructed in Chapter 3.

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The next chapter moves on to describe a new supertree of the Dinosauria and describes the results found from the first quantitative study of diversification of the Dinosauria.

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Chapter 6

Dinosaurs and the Cretaceous Terrestrial Revolution

This chapter has been submitted as a paper to Proceedings of the National Academy of Sciences.

6.1 Abstract

Dinosaurs were never more diverse than in the last 18 million years before their extinction, just as modern, angiosperm-dominated ecosystems were establishing themselves. This radiation of flowering plants was key to the Cretaceous Terrestrial Revolution (CTR), a time when lizards, birds, mammals and insects were adapting to the new ecological opportunities on offer. Others argue that dinosaurs were in decline long before their ultimate extinction. We show here that both views are incorrect, that the apparent explosion of dinosaurian diversity is a result of sampling, but that the group was not declining either. Results from the first quantitative study of diversification applied to a new supertree of dinosaurs suggest that this apparent burst in diversity at the end of the Cretaceous is a sampling artefact. In fact, dinosaurs showed most of their major diversification shifts in the first third of their history. Dinosaurs then were not progressively declining at the end of the Cretaceous; nor were they profiting from the new ecological opportunities offered by the CTR.

6.2 Introduction

Dinosaurs are icons of success and failure. According to a long-standing hypothesis (Sloan et al., 1986; Sarjeant and Currie, 2001), the group was in decline long before its extinction at the end of the Cretaceous period, 65 Ma (million years) ago. However, new evidence (Wang and Dodson, 2006) suggests a major increase in diversification during the Campanian and Maastrichtian, spanning approximately the last 18 Ma of the Cretaceous, and so emphasizes the dramatic nature of their apparently sudden extinction at the end of the Cretaceous. This

102 CHAPTER 6: DINOSAUR SUPERTREE AND DIVERSIFICATION KATIE DAVIS diversification has been seen as evidence that dinosaurs were part of the Cretaceous explosion of terrestrial life (Weishampel et al., 2004) characterized by, among others, the rise of flowering plants, social insects, butterflies, as well as modern groups of lizards, mammals, and possibly birds (Hedges et al., 1996; Grimaldi, 1999; Dilcher, 2000; Fountaine et al., 2005; Bininda-Emonds et al., 2007).

The Cretaceous period (145-65 Ma ago) has long been regarded as a time of major reorganization and modernisation of ecosystems. In the marine realm, these ecosystem changes have been named collectively the Mesozoic Marine Revolution (Vermeij, 1977), characterized by the appearance of new groups of planktonic organisms (e.g. coccoliths, foraminifera, dinoflagellates, diatoms) and new predators among crustaceans, teleost fishes, and marine reptiles. It has been postulated (Vermeij, 1987) that the emergence of such predators selectively favoured the appearance of thicker exoskeletons as a defensive measure in prey groups such as bivalves, gastropods, and echinoids. The evolution of land organisms was also characterized by a Cretaceous Terrestrial Revolution (CTR), as we term it here, marked by the replacement of ferns and gymnosperms by angiosperms (Dilcher, 2000). The huge radiation of angiosperms provided new evolutionary opportunities for pollinating insects, leaf-eating flies, as well as butterflies and moths, all of which diversified rapidly (Grimaldi, 1999). Among vertebrates, lizards, snakes, crocodilians, modern placental mammal superorders, and primitive groups of birds underwent major diversifications (Hedges et al., 1996, Fountaine et al., 2005, Bininda-Emonds et al., 2007) although the timing of appearance of modern bird orders remains controversial (Hedges et al., 1996; Dyke, 2001).

Dinosaur evolution was characterized by the appearance of truly spectacular new forms. Giant sauropods, the dominant herbivores of the Jurassic, were joined by new kinds of ornithischians at the beginning of the Cretaceous. Subsequent new waves of diversification at the beginning of the Late Cretaceous (some 100 Ma) produced a diverse fauna of hadrosaurs, ceratopsians, ankylosaurs, and pachycephalosaurs, among herbivores, as well as new theropod groups, including the giant tyrannosaurs and carcharodontosaurs, and the smaller troodontids, dromaeosaurs, and ornithomimosaurs. Qualitatively then dinosaurs appear to have been part of the CTR.

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As is commonly the case, studies of dinosaur diversity through time have suffered from the lack of a conceptual framework in which ‘diversification’ is defined, detected, and quantified. Furthermore, a proper evaluation of sampling biases (Raup, 1972; Benton et al., 2000; Alroy et al., 2001) has not been taken into account. Two key sampling issues are that the fossil record of a group may be truncated (i.e. lacking its youngest and/or oldest members) and that the number of observed taxa depends to some extent on sampling intensity (a proxy for this is the number of localities investigated or the number of specimens collected). Here, we address both issues, and use analytical protocols to minimise or exclude them.

At the heart of our analysis is a new supertree of dinosaurs, which represents a development and expansion of an earlier study (Pisani et al., 2002), and consists of 440 species (some 70% of the total number of valid species), and an additional 15 undescribed or indeterminate forms. Use of large trees in diversification analyses is commonly two-pronged. Previous workers have used them to fill implied gaps in the fossil record and correct raw species richness counts accordingly (Weishampel and Jianu, 2000; Upchurch and Barrett, 2005), though never for the whole group. A completely different approach is to use tree shape to search for and date perturbations consistent with divergence from a simple birth-death model (Forest et al., 2007; Ruta et al., 2007). Here we use both approaches to test whether dinosaurs responded to the CTR, by comparing the magnitude and rates of their diversification in the Cretaceous with their diversification characteristics in the and Jurassic.

6.3 Methods

6.3.1 Supertree Reconstruction

We expanded significantly upon the previous list of source trees (Pisani et al., 2002) with publications up to the end of 2006. This list was then shortened by removing those trees without a corroborating cladistic analysis (i.e. a matrix and character list available either as part of the publication itself, as an electronic appendix, or explicitly available – and obtained – from the author). Retention of this information allowed determination of redundant source trees (Bininda-Emonds et al., 2004),

104 CHAPTER 6: DINOSAUR SUPERTREE AND DIVERSIFICATION KATIE DAVIS reinsertion of outgroup(s) discarded in published figures and the re-running of analyses where the source publication did not provide a standardized (strict) consensus tree. Not all trees could be considered novel, and hence independent (Bininda-Emonds et al., 2004). When one analysis clearly superseded an earlier work we retained the later tree and discarded the original. When multiple later works had equal claim we included them all, but weighted them in tree searches so that their net contribution was equal to one independent tree. Overall these filters led to a strong skew in the data toward more recent analyses (Figure 6.1), greatly enhancing the chances of recovering a tree that represents current consensus.

Figure 6.1: The year of publication of source trees shows a strong skew among included trees towards more recent analyses. The three major peaks (1990, 1999, 2004) correspond to the publication of The Dinosauria first edition (Weishampel et al., 1990), a Science review paper (Sereno, 1999) and The Dinosauria second edition (Weishampel et al., 2004) respectively.

Unlike the previous effort (Pisani et al., 2002) we chose to produce a species-level supertree. This decision was bolstered by an authoritative recent compilation of valid names (Weishampel et al., 2004) that served as our primary reference for nomina dubia, which were purged, and junior synonyms, which were replaced with their

105 CHAPTER 6: DINOSAUR SUPERTREE AND DIVERSIFICATION KATIE DAVIS senior counterpart. Birds above Archaeopteryx and non-dinosaurian taxa were also purged from the source trees. Supraspecific taxa were replaced with all species that could be unequivocally assigned to that higher taxon based on the labelled nodes of source trees (Page, 2004), with the exception of genera, which were replaced by their type species, or, if more than one species exists, then the most completely known. Each source tree was processed in this way and both a tree (Page, 1996) and XML file produced. The latter contained metadata about the source publication, taxa and characters, ensuring a consistent standard of data collection and audit trail for future updates. Standard (Baum, 1992) and Purvis (Purvis, 1995) MRP matrices were then produced using a modified version of SuperMRP.pl (Bininda-Emonds et al., 2006), Radcon (Thorley and Page, 2000) and CLANN (Creevey and McInerney, 2005).

Tree searches were performed following an established protocol (Pisani et al., 2002; Pisani et al., 2007). First, 5000 heuristic searches were performed in PAUP* 4.0b10 (Swofford, 2002) with the MulTree option turned off. Trees obtained from these searches were saved and swapped using the tree bisection reconnection algorithm, and the MulTree option on (to retain multiple equally optimal trees). The Parsimony Ratchet (Nixon, 1999) could not find a better tree. The split fit supertree (Wilkinson et al., 2005) was built analysing the standard MRP matrix using Mix, which is part of the Phylip package (Felsenstein, 2000). To enforce Mix to run a compatibility analysis, the threshold parsimony option was set to 2. One hundred heuristic searches were performed, and characters were weighted (as described above) using a specifically generated weight file (Felsenstein, 2000).

In order to obtain a well-resolved tree we undertook some post hoc taxon pruning where poorly constrained species, producing unacceptably high numbers (> 5000) of equally likely supertrees, were removed. Choosing a tree for diversity analyses was based on overall supertree support. Here we used the V1 index (Wilkinson et al., 2005), which indicated that support was highest for the standard MRP supertree (Figure 6.2).

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Figure 6.2: Standard MRP tree with clade labels. Majority-rule with minority components consensus tree of the reduced standard MRP matrix showing the major clades. Abbreviated clade names are: Mam. = Mamenchisauridae, Br. = Brachiosauridae, Her. = Herrerasauridae, Compsog. = "Compsognathoidea", Ornithomimo. = Ornithomimosauria, Therizino. = Therizinosauroidea, Alvar. = Alvarezsauridae and, Troodon. = Troodontidae.

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6.3.2 Diversification Metrics

We calculated the percentage change, per million years, of global species richness among 12 successive time bins of subequal duration for three different datasets: 1) a recent database of the known dinosaur record (Weishampel et al., 2004), 2) the same dataset but with some species’ first appearances extended back in time as implied by a sister-group relationship with an older taxon (Norell, 1992) in the supertree and, 3) a subsampled dataset.

Subsampling methods have played an important role in ecology (Gotelli and Colwell, 2001) and palaeoecology (Raup, 1975; Tipper, 1979) as they offer the opportunity to examine the effects of taxonomic sampling on measures of species richness. Methodologically our approach is equivalent to setting the global quality of the record as equal to that of the worst part of it. Here we subsample the same dataset as above 1,000 times and record the number of species observed in a sample of 35 occurrences each time. Subsampling was performed using custom-built code (available on request from the lead author) in the freely available statistical programming language ‘R’ 1. Note that in all cases diversification rates for each time bin were calculated using SymmeTREE version 1.0 (Chan and Moore, 2005). No diversification rate was calculated for the first bin as there are no unequivocal dinosaurian fossils, or for the second as there is no previous richness value – diversification is infinite. SymmeTREE implements a tree topology-dependent method for detecting diversification rate shifts (i.e. significant changes in lineage branching, based upon differences in the number of taxa and degree of imbalance on the left and right branches subtended by tree nodes) (Ruta et al., 2007).

Phylogenetic shifts in diversification were also detected using SymmeTREE version 1.0 (Chan and Moore, 2005). In order to avoid non-monophyly biases associated with the exclusion of birds a ‘dummy’ branch representing a composite phylogeny of 72 Mesozoic species was inserted at the node subtending Archaeopteryx + Jinfengopteryx . Polytomies were treated as soft, with the size-sensitive ERM (Equal

1 http://cran.r-project.org

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Rates Markov) algorithm set to perform 10,000 random resolutions per individual node and 1,000,000 random resolutions for the entire tree. Internal branches within the phylogeny on which diversification shifts are inferred to have occurred were identified using the ∆2 shift statistic (a measure of the likelihood that a shift occurred). This process was repeated for time-slices of the whole tree as described in Ruta et al . (2007) to avoid violating the ERM-model.

6.4 Results

6.4.1 Ghost Ranges Account for Some Irregularities in the Diversity Curves

The supertree of dinosaur species is plotted on a geologic time scale (Gradstein et al., 2004) (Figure 6.3a and Appendix G) split into twelve approximately equal- length time bins to assess the extent of ghost ranges (Norell, 1992). Ghost ranges, minimal basal stratigraphic range extensions implied by the geometry of the phylogenetic tree, indicate missing fossil data, and they allow us to correct diversity profiles for the group through the Mesozoic, and to compare diversification rates, the proportional change in observed species richness as a function of time, at different points (Figure 6.3b): note how the addition of ghost ranges smoothes the curve. In particular, peaks in observed diversification rate in the Norian and Campanian- Maastrichtian (bins 3 and 12) are greatly reduced when ghost ranges are introduced. This is a minimal correction that does not take account of unknown taxon ranges before the first appearance of the older of a pair of sister groups. In addition of course, this correction does not address possible upward range extensions. However, peaks in the earliest, Middle and Late Jurassic are still observed after introduction of ghost ranges (Figure 6.3).

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Figure 6.3: Results of different analyses of dinosaur diversification. a) A summary version of the supertree used here (Figure 6.2 for full tree); the eleven statistically significant diversification shifts present in both the entire tree and at least one time-slice are marked with white arrows denoting the branch leading to the more speciose clade. Taxa in bold represent the collapsing of a larger clade, the size of which is indicated in parentheses. An ‘*’ indicates the collapsing of a paraphyletic clade and a ‘†’ an extant clade (i.e. birds). b) Diversification rates based on the raw record (blue), the raw record plus additional ‘ghost’ ranges (green) and

subsampled data (red; see text). c) Mean values of ∆2 shift statistic through time (see text).

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6.4.2 Correction for Sampling Removes Some Extreme Diversity Peaks

To test whether these peaks represent real diversification episodes or are simply the result of unusually intense sampling, we considered the number of dinosaur localities in each stratigraphic stage (Weishampel et al., 2004). If localities sampled determine generic diversity, then the apparent diversification measures, once corrected for locality numbers, might be levelled. Our approach represents a subsampling method similar to rarefaction. Rarefaction methods have played an important role in ecology (Gotelli and Colwell, 2001) and palaeoecology (Raup, 1975 ; Tipper, 1979) as they offer the opportunity to examine the effects of taxonomic sampling on measures of species richness. Here we measure sample size as the total number of species occurrences by locality for each of our twelve time bins. When the same diversification calculations are applied to these subsamples (the mean and 95% bounds of which are plotted in Figure 6.3b), much lower values are recovered. These results suggest, but do not prove, that diversity estimates are heavily influenced by sampling, and further that the ghost range, i.e. tree-based, correction is indeed minimal. It follows that the fluctuations in diversification rate may not necessarily reflect evolutionary signal, and these must be tested rigorously.

6.4.3 Diversification Shifts are Concentrated in the Lower Half of the Dinosaur Tree

An alternative approach relies instead on phylogenetic tree shape. Phylogeny is determined by the available taxa and the inferred pattern of relationships, and phylogenetic tree shape reflects large-scale variations in speciation and extinction rates (Mooers and Heard, 1997). Topological methods (Bininda-Emonds et al., 1999, Katzourakis et al., 2001; Chan and Moore, 2005; Jones et al., 2005) may be used to identify diversification rate shifts in phylogenetic trees, based on comparison between the observed tree and one expected under an ERM model. An ERM-model assumes that sister groups should contain a similar number of taxa as they originated at the same time; thus, if one group is significantly more speciose than the other a diversification rate shift may be inferred.

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Analysis of diversification rates in the supertree using SymmeTREE shows that statistically significant ( p < 0.05) and substantial (0.05 < p < 0.1) diversification shifts (i.e. multiplications of evolutionary lineages) were heavily concentrated in the first third of the evolution of the clade Dinosauria (Figure 6.3b and Appendix G). The majority are at the base of the Dinosauria, in the Late Triassic to Early Jurassic (230-175 Ma), and mark the origin of major clades (10 significant shifts; Genasauria, Eurypoda, Cerapoda, Sauropodomorpha, Neotheropoda, Tetanurae, Coelurosauria, Maniraptoriformes, , Oviraptorosauria). Later statistically significant diversification shifts occur in the Aalenian (1; Neosauropoda), Kimmeridigian (2; Ankylosauria, Eumaniraptora), Turonian (1; Euhadrosauria), and Campanian (1; Ceratopsidae). Of the 15 significant and 11 substantial diversification shifts, there are two significant and two substantial shifts in the Triassic, 11 significant and seven substantial in the Jurassic, and two significant, and two substantial shifts in the Cretaceous. This confirms that most diversification among Dinosauria occurred early, and very little is detected in the second two-thirds of their history, the 120 Ma from the Middle Jurassic onwards. When the mean ∆2 shift statistic, which represents the likelihood that a shift occurred, is plotted against time (Figure 6.3c) there is a peak value of 0.58 during the Rhaetian-Sinemurian (Bin 4; 205-190 Ma) followed by an overall decrease towards the present. Two-thirds of significant pairwise comparisons between ∆2-values (Kruskal-Wallis test; p < 0.05) show bins 4 and 5 (Rhaetian-Aalenian; 205-170 Ma) to have higher likelihoods of a diversification shift.

The robustness of these results was tested further by ‘time-slicing’ our tree to avoid issues surrounding violation of the ERM-model’s assumptions (Ruta et al., 2007). This involved creating eleven separate trees, one for each of our time bins, which included only the taxa that existed, or are posited to have existed, at that time. These results strongly support our whole-tree analysis, with 11 of the 15 significant shifts also occurring in the time-sliced trees. Only one novel significant shift was discovered in the time-sliced trees, coincident with the origin of Lithostrotia in the

Valanginian (140 Ma). Again, the highest mean ∆2 shift statistic (0.69) was found in bin 4, with a general decrease going forwards in time. Similarly, over half of the significant pairwise comparisons between ∆2-values show time bins 4 and 5 to have had higher likelihoods of a diversification shift. All results are robust even if the

112 CHAPTER 6: DINOSAUR SUPERTREE AND DIVERSIFICATION KATIE DAVIS controversial taxon Eshanosaurus , which is here placed as a therizinosaur and is responsible for dating four of the significant shifts (Tetanurae, Coelurosauria, Maniraptoriformes, Maniraptora), is removed.

6.5 Discussion

6.5.1 Diversification Shifts are not Always Concentrated in the Lower Half of a Tree

Geometric arguments might suggest that it is inevitable to find the majority of diversification shifts low in a tree. To an extent, of course, there must be statistically- significant diversification shifts at the base of the tree, as the founding taxa within the clade split and major branches become established. Bats, for example, show a similar early diversification pattern (Jones et al., 2005), but ants do not (Forest et al., 2007). The reason is that clades do not inevitably stop diversifying once they have become established. Studies of the distribution of clade shapes (Gould et al., 1977; Valentine, 1990; Uhen, 1996; Nee, 2006) show all possible shapes (after paraphyly has been accounted for), ranging from bottom-heavy to top-heavy, tall and thin, short and fat, and even spindle-shaped, where the clade has been hit hard by an extinction event or other bottlenecking crisis, and has then recovered. In the case of Dinosauria here, the clade continues to expand up to the end of the Cretaceous, and yet, statistically speaking, the Cretaceous expansion cannot be distinguished from the normal expectation of an ERM.

6.5.2 Sampling Must be Taken into Account

The fossil record of continental vertebrates is clearly patchy, with large temporal gaps between sampling horizons. The seriousness of sampling bias is debated, with opinion ranging from assumptions that the fossil record offers more of a geological than a biological signal (Raup, 1972; Alroy et al., 2001; Peters and Foote, 2002) to acceptance that sampling error does not much modify the apparent macroevolutionary patterns (Sepkoski et al., 1981; Benton, 1999). Comparisons of cladograms with the fossil record show good congruence in most cases (Norell and Novacek, 1992; Benton et al., 2000), so suggesting that the biological signal,

113 CHAPTER 6: DINOSAUR SUPERTREE AND DIVERSIFICATION KATIE DAVIS assessed at the correct scale, is probably adequately represented. Current efforts (Smith, 2007) focus on methods to quantify sampling bias, and to determine parts of the fossil record signal that stand out after sampling has been considered.

In this paper, we have used the number of dinosaur localities in each time bin as a crude measure of sampling. Other measures could have been area of rock exposure, volume of rock deposited per unit time, total number of geological formations whether fossiliferous or not, or intensity of worker effort – number of palaeontologists, for example. All such measures are of course themselves subject to debate, and there is a risk that the crude use of a sampling measure to correct diversity figures automatically may be sufficiently heavy-handed that any biological signal is overwhelmed (Peters and Foote, 2002; Smith, 2007). For example, there is doubtless a species-area effect (Smith, 2001), in which rock area or volume, or number of formations, is linked with the diversity of life. For example, during times of high sea level, continental margins flood, and species on the continental shelf increase in abundance and diversity. To ‘correct’ those diversity figures by dividing by shelf area or rock volume, could perfectly remove the biological signal.

Our solution, to offer both the raw data and the sampling-modified data (Figure 6.3b), allows comparison of the data without making an assumption that one or the other version is correct, and points to the need for further examination of each of the undoubted biases in our understanding of this fossil record. Before applying a correction factor, we need evidence of how collecting intensity (i.e. number of palaeontologists; number of field days), rock availability, and other sampling factors affect the results. The relationship is almost certainly not linear, and that in itself speaks against crude application of sampling corrections. For example, discovery curves for dinosaurs and other fossil taxa, when calibrated against worker effort (Tarver et al., 2007), show a classic logistic shape, where huge efforts at present do not necessarily yield huge numbers of new fossils.

6.5.3 Dinosaurs and the Cretaceous Terrestrial Revolution (CTR)

Previous studies have been equivocal about whether dinosaurs ate angiosperms. The Late Cretaceous expansion of dinosaurian diversity, founded especially on the

114 CHAPTER 6: DINOSAUR SUPERTREE AND DIVERSIFICATION KATIE DAVIS diversification of herbivorous dinosaurs such as hadrosaurs, ceratopsians, and ankylosaurs, might have suggested that these groups, all of which either arose or diversified substantially only after the origin of angiosperms in the mid Cretaceous, were angiosperm specialists. Bakker (1978), for example, argued that the ornithopods of the Early Cretaceous fed close to the ground, and so favoured gymnosperms in their diet. Because of their intense low-level feeding, the only plants that could survive the onslaught were the earliest angiosperms that held their reproductive organs close to the ground. And so, in his words, dinosaurs invented flowers.

This view is disputed, and there is actually very limited evidence to demonstrate that Cretaceous dinosaurs fed on angiosperms (Barrett and Willis, 2001). The patterns of rises and falls in the diversity of Cretaceous dinosaurs and Cretaceous plants, as well as their palaeogeographic distributions, do not suggest any correlation. Coprolites, fossil faeces, are rare, and often cannot be attributed to their producer; Cretaceous examples include some with traces of the angiosperm biomarkers, oleananes, whereas others contain exclusively gymnosperm material. An Early Cretaceous ankylosaur, Minmi , has been reported (Molnar and Clifford, 2000) with remnants of angiosperm fruits in its gut, and some remarkable dinosaurian coprolites from show that some dinosaurs ate early grasses (Prasad et al., 2005). Fossil occurrences and studies of the teeth and postulated jaw functions of herbivorous dinosaurs suggest that angiosperms were a part of the diet of many dinosaurs, but that gymnosperms were still possibly the major constituent in many cases (Barrett and Willis, 2001). Plant-eating insects and mammals very likely benefited more from the new sources of plant food.

Detailed studies of dinosaurian herbivory and plant evolution (Barrett and Willis, 2001) had already suggested there was limited evidence that angiosperm diversification drove the Cretaceous diversification of dinosaurs. Our new evidence confirms that the Cretaceous Terrestrial Revolution was key in the origination of modern continental ecosystems, but that the dinosaurs were not a part of it. Hadrosaurs and ceratopsians showed late diversifications, but not enough to save the dinosaurs from their fate.

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Chapter 7

Discussion and Conclusions

7.1 Introduction

This thesis has dealt with the construction of a large-scale supertree of extant and extinct avian taxa at species level. It is the largest such supertree ever constructed (to the author’s knowledge) and contains over 5000 taxa. A robust protocol for collecting and processing source data for such as study has been detailed and tested. This protocol was also used to construct an updated, species-level supertree of dinosaurs containing 440 taxa. Put together, this constitutes an almost 6000 taxa species-level supertree of the archosaurs. This chapter gives a brief summary of the main findings of this thesis by assessing the questions asked in Chapter 1 and summarising the main conclusions of the study. It concludes with suggestions for future work.

7.2 Conclusions

The questions set out in Chapter 1 are reiterated and answered here.

1. Can a protocol for constructing supertrees be developed that is both methodologically robust and easy to implement?

Chapter 3 describes the protocol designed and implemented in this thesis. It was observed that the protocol described by Bininda-Emonds et al. (2004), although largely adequate and a novel idea, contained some gaps and a lack of suggestions for practical implementation. One such gap was how to deal with non-independent source trees either by combining into a “mini-supertree” (as in Bininda-Emonds et al., 2004) or by down-weighting the trees by an appropriate factor. It was found that it is better to combine non-independent source trees than it is to down-weight those source trees as statistical results from MASTd and triplet fit of the supertree(s) to the source trees showed that the supertree constructed from combined data gave a result

116 CHAPTER 7: DISCUSSION AND CONCLUSIONS KATIE DAVIS more concordant with the source trees than that from down-weighting the data. Additionally, it was much faster both to implement the combined method and analyse the resulting character matrix. For the main supertree analysis in Chapter 4, using this protocol reduced the taxa number from 7384 to 5274 by removing higher taxa, vernacular names and synonyms. Removing these taxa increases overlap between the source trees and hence is likely to produce a better result.

The protocol was straightforward to implement, but time-consuming. Scripts were used to largely automate the process. It took significantly longer to collect and process data ready for supertree construction than it took to collect and process data ready for supermatrix analysis (Chapter 5).

2. Does this protocol result in supertrees that are good representations of the source data?

Both supertrees constructed in Chapter 3 gave reasonable, sensible results with a minimum of spurious groups. There were no surprises in the results and both conformed well to currently accepted views on galliform phylogeny. Using the protocol for species-level trees of both Dinosauria and Aves produced sensible trees with few novel clades (given their size). In addition, a molecular-only supertree of the Galliformes was produced using the protocol. This resulted in a phylogeny very similar to that made via supermatrix methods (see below). Both these phylogenies (supertree and supermatrix) were very similar to the supertrees constructed in Chapter 3.

3. Can a supertree of all Aves be constructed at species-level using this protocol?

The species-level supertree of Aves contains 5274 taxa, both extinct and extant, more than half of all known extant taxa. The results were sensible, giving a reasonable summary of the current knowledge of avian phylogeny. Due to the stringent data processing methods, it is possible to pinpoint areas where primary data collection and analysis are required much more clearly. Many of these areas were identified by the presence of novel clades, which, on inspection, were evidently the result of poor taxonomic sampling. Other novel clades were as a result of the inclusion of fossil taxa, the only solution here is for more fossils to be described and

117 CHAPTER 7: DISCUSSION AND CONCLUSIONS KATIE DAVIS included in phylogenetic analyses. Finally, there were some spurious groups that can not be easily explained. These could be due to undesirable properties of MRP or may be resolved simply by further analysis, as the current analysis was, by necessity, limited to a run time of just 12 hours. However, even with this limited run time, the tree is a good estimate of current understanding of bird phylogeny and will be very useful in future studies.

4. Can community-based tree-building help speed up the process in finding shorter tree?

The community aspect of the project was unfortunately not very successful. A few data problems were found by others (taxon duplication and a few erroneous trees), but only one other person uploaded a final tree. It is surprising that the project did not attract more attention as a large species-level supertree of birds is very much in demand at the present time.

5. Do supertree methods compare favourably with trees found from supermatrix analyses? Which, if either, produces superior results?

The results from both supermatrix and supertree analysis of molecular data were very similar (Chapter 5). Both trees were analysed in the same way as the Galliformes supertrees in Chapter 3 (i.e. compared to independent small-scale phylogenies using triplets and MASTd) and show that there is no statistically significant difference between the tree constructed from a supermatrix and that constructed from a supertree analysis, i.e. each represents the input source data as well as the other. Both trees were very similar in terms of large-scale relationships. Each gave sensible results and no spurious groups were identified. The higher-level relationships did not differ to those found in the taxonomically more inclusive trees constructed in Chapter 3. In this way, the two methods are complementary as suggested by Bininda-Emonds (2004).

6. Can a new, updated supertree of the Dinosauria shed light on dinosaur diversification throughout the Cretaceous?

The dinosaur supertree was created using a slightly modified version of the protocol designed and described in Chapter 3. The protocol was modified (in terms of the

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XML file structure and down-weighted non-independent source trees rather than combining) in order to suit information related to fossil taxa. This was the first quantitative study of diversification applied to a supertree of dinosaurs and the results show that an apparent burst in diversity at the end of the Cretaceous is a sampling artefact and that dinosaurs show most of their major diversification shifts in the first third of their history. Dinosaurs then were not progressively declining at the end of the Cretaceous as previously thought; nor were they profiting from the new ecological opportunities offered by the Cretaceous modernisation of terrestrial ecosystems.

7.3 Further work

7.3.1 Further analysis of the tree

It would be interesting to investigate the tree further by running the analysis for a longer period of time as the current analysis was, by necessity, limited to a run time of just 12 hours. However, even with this limited run time, the tree is a good estimate of current understanding of bird phylogeny and will be very useful in future studies. It would also be of value to continue updating the tree, which is straightforward due to the data collection methods employed. The current tree includes all avian phylogenies up to January 2006 and more have been published since then. As phylogenies are continually being published, the supertree will always become out- of-date in a short period of time, but it is still valuable as a "snapshot” of currently accepted views of phylogeny.

7.3.2 Dating of the tree

An interesting study would be to date the tree as in Bininda-Emonds et al. (2007) mammal supertree, which was then used analyse to how extant lineages accumulated through time. This could be particularly interesting as the avian supertree presented here has incorporated fossils, something not covered by Bininda-Emonds et al. (2007). A supertree with dates could be used to explore the question of whether modern birds originated and diversified in the Tertiary or whether modern lineages

119 CHAPTER 7: DISCUSSION AND CONCLUSIONS KATIE DAVIS originated in the Cretaceous and passed through the K-T boundary largely unaffected.

7.3.3 Taxonomy issues

This supertree of birds is a very comprehensive study of avian taxonomy; with over 5000 taxa in the final supertree. However, in order to create the best supertree possible the data were heavily sanitised; with replacement of synonyms and standardisation of names. Use of a consistent taxonomy is important because allowing synonyms and other invalid taxa to remain will artificially inflate the taxa number and, crucially, reduce the amount of overlap between source trees in a supertree analysis. From a wider viewpoint, use of a standardised taxonomy is essential in conservation issues.

For the main supertree analysis in Chapter 4, using this protocol reduced the taxa number from 7384 to 5274 by removing higher taxa, vernacular names and synonyms. This highlights the issues present in avian taxonomy, i.e. that there are a huge amount of invalid names present and this will obviously have an effect on the building of any phylogeny. For this thesis, both the standardised (regarding taxonomy) and original (as in the source trees) data were retained, which gives an opportunity to assess how “good” avian taxonomy is in terms of taxonomic stability and integrity. An investigation into the issues surrounding avian taxonomy was beyond the scope of this study but would be a worthwhile use of the large datasets collected, and retained, for this thesis.

7.3.4 Large-scale avian supermatrix

An interesting question is whether a species-level avian supermatrix could be constructed to the same, or near, level of taxonomic coverage as the supertree presented in this thesis. Supertree proponents often cite the inability to create such large supermatrices as a reason to build supertrees but it would be interesting to see just how large a matrix would be possible. As shown in Chapter 5, it would be relatively easy to assimilate the relevant data ready for analysis but computational time is likely to be the limiting factor.

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It would also be interesting to download molecular data from GenBank and then use this to construct both individual source trees for each gene and then a supermatrix. The source trees could then be used to build a supertree, the results of which could then be compared to the supermatrix, as in Chapter 5, to look at how well each tree represents the source data. This was beyond the scope of this study with regards to time limitations, and also does not perhaps reflect “real-life” situations, in which source trees are not necessarily constructed under ideal conditions.

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135 APPENDIX A: TAXONOMIC NAME SERVER KATIE DAVIS

Appendix A

List of names not found by Taxonomic Name Server

The table below shows queried names not found by the Taxonomic Name Server (1 st column). The correct name is shown in the second column (which is not necessarily different fro the queried name). The 3 rd column highlights those taxa which are extinct.

Queried name Corrected name Acrocephalus scirpaceus avicenniae Acrocephalus scirpaceus avicenniae Acrocephalus stentoreus australis Acrocephalus australis Acrocephalus stentoreus harteri Acrocephalus stentoreus harteri Acrocephalus stentoreus levantina Acrocephalus stentoreus levantina Aegialornis gallicus Aegialornis gallicus Extinct Aegialornis leenhardti Aegialornis leenhardti Aegintha temporalis Neochmia temporalis Aegotheles albertisi albertisi Aegotheles albertisi albertisi Aegotheles albertisi salvadorii Aegotheles albertisi salvadorii Aegotheles bennettii affinis Aegotheles bennettii affinis Aegotheles bennettii bennettii Aegotheles bennettii bennettii Aegotheles bennettii plumiferus Aegotheles bennettii plumiferus Aegotheles bennettii terborghi Aegotheles bennettii terborghi Aegotheles bennettii wiedenfeldi Aegotheles bennettii wiedenfeldi Aegotheles novaezealandiae Aegotheles novaezealandiae Aegotheles tatei Euaegotheles tatei Aegotheles wallacii gigas Aegotheles wallacii gigas Aegotheles wallacii wallacii Aegotheles wallacii wallacii Aepyornis Aepyornis Extinct Aerodramus brevirostris vulcanorum Aerodramus brevirostris vulcanorum Aerodramus maximus lowi Aerodramus maximus lowi Aerodramus salangana natunae Aerodramus salangana natunae Aerodramus terraereginae Aerodramus terraereginae terraereginae terraereginae Aerodramus vanikorensis lugubris Aerodramus vanikorensis lugubris Aerodramus vanikorensis Aerodramus vanikorensis palawanensis palawanensis Agelaioides badius Molothrus badius Agelaius phoeniceus assimilis Agelaius assimilis Agelasticus cyanopus Agelaius cyanopus Agelasticus thilius Agelaius thilius Agelasticus xanthophthalmus Agelaius xanthophthalmus Aidemedia chascax Aidemedia chascax Extinct Aidemedia lutetiae Aidemedia lutetiae Extinct Aidemosyne modesta Aidemosyne modesta

136 APPENDIX A: TAXONOMIC NAME SERVER KATIE DAVIS

Akialoa lanaiensis Akialoa lanaiensis Extinct Akialoa obscurus Akialoa obscurus Extinct Akialoa upupirostris Akialoa upupirostris Extinct Alario alario Serinus alario Alcedo cyanopecta cyanopecta Alcedo cyanopectus cyanopectus Alcedo cyanopecta nigrirosta Alcedo cyanopectus nigrirostris Alle alle polaris Alle alle polaris Amazona aestiva aestva Amazona aestiva aestiva Amazona aestiva xanthopteryx Amazona aestiva xanthopteryx Amazona albifrons albifrons Amazona albifrons albifrons Amazona albifrons nana Amazona albifrons nana Amazona albifrons saltuensis Amazona albifrons saltuensis Amazona auropalliata auropalliata Amazona auropalliata auropalliata Amazona auropalliata parvipes Amazona auropalliata parvipes Amazona autumnalis autumnalis Amazona autumnalis autumnalis Amazona autumnalis lilacina Amazona autumnalis lilacina Amazona farinosa farinosa Amazona farinosa farinosa Amazona farinosa guatemalae Amazona farinosa guatemalae Amazona farinosa inornata Amazona farinosa inornata Amazona farinosa virenticeps Amazona farinosa virenticeps Amazona festiva bodini Amazona festiva bodini Amazona leucocephala leucocephala Amazona leucocephala leucocephala Amazona ochrocephala nattereri Amazona ochrocephala nattereri Amazona ochrocephala nattereri Amazona ochrocephala nattereri Amazona ochrocephala ochrocephala Amazona ochrocephala ochrocephala Amazona ochrocephala ochrocephala Amazona ochrocephala ochrocephala Amazona ochrocephala xantholaema Amazona ochrocephala xantholaema Amazona ochrocephala xantholaema Amazona ochrocephala xantholaema Amazona oratrix belizensis Amazona oratrix belizensis Amazona oratrix hondurensis Amazona oratrix hondurensis Amazona oratrix oratrix Amazona oratrix oratrix Ambiortus Ambiortus Extinct Amitabha urbsinterdictensis Amitabha urbsinterdictensis Extinct Ampelion sclateri Doliornis sclateri Amytornis barbatus barbatus Amytornis barbatus barbatus Amytornis barbatus diamantina Amytornis barbatus diamantina Amytornis purnelli purnelli Amytornis purnelli purnelli Amytornis striatus merrotsyi Amytornis striatus merrotsyi Amytornis striatus striatus Amytornis striatus striatus Amytornis textilis modestus Amytornis textilis modestus Amytornis textilis myall Amytornis textilis myall Anabazenops dorsalis Automolus dorsalis Anatalavis Extinct Anatalavis oxfordi Anatalavis oxfordi Extinct Anneavis anneae Anneavis anneae Extinct Anser rubrirostris Anser anser Aplopelia simplex Columba larvata simplex Apsaravis Apsaravis Extinct Apsaravis ukhaana Apsaravis ukhaana Extinct Apteryx mantelli Apteryx australis Aquila pomarina hastata Aquila pomarina hastata

137 APPENDIX A: TAXONOMIC NAME SERVER KATIE DAVIS

Archaeopteryx Archaeopteryx Extinct Archaeopteryx lithographica Archaeopteryx lithographica Extinct Argillornis emuinus Argillornis emuinus Extinct Argornis caucasicus Argornis caucasicus Asthenes arequipae Asthenes dorbignyi arequipae Asthenes huancavelicae Asthenes dorbignyi huancavelicae Asturina nitida costaricensis Asturina nitida costaricensis Asturina nitida nitida Asturina nitida nitida Asturina nitida plagiata Asturina nitida plagiata Atlapetes latinuchus Atlapetes latinuchus Avisaurus archibaldi Avisaurus archibaldi Extinct Avisaurus gloriae Avisaurus gloriae Extinct Baptornis advenus Baptornis advenus Extinct Barnardius barnardi barnardi Barnardius barnardi barnardi Barnardius barnardi macgillivaryi Barnardius barnardi macgillivaryi Barnardius barnardi whitei Barnardius barnardi whitei Berenicornis Berenicornis Blythipicus pyrrhotis sinensis Blythipicus pyrrhotis sinensis Bocagia minuta Tchagra minuta Bowdleria punctata Megalurus punctatus Bradornis mariquensis Melaenornis mariquensis Branta hrota Branta bernicla Breagyps clarki Breagyps clarki Extinct Bubo zeylonensis Ketupa zeylonensis Bucorvus cafer Bucorvus leadbeateri Buteo albicaudatus colonus Buteo albicaudatus colonus Buteo albonotatus albonotatus Buteo albonotatus albonotatus Buteo brachyurus brachyurus Buteo brachyurus brachyurus Buteo buteo arrigonii Buteo buteo arrigonii Buteo buteo socotrae Buteo buteo socotrae Buteo jamaicensis costaricensis Buteo jamaicensis costaricensis Buteo japonicus Buteo buteo japonicus Buteo japonicus toyoshimai Buteo buteo toyoshimai Buteo magnirostris griseocauda Buteo magnirostris griseocauda Buteo magnirostris magniplumis Buteo magnirostris magniplumis Buteo magnirostris saturatus Buteo magnirostris saturatus Buteo polyosoma exsul Buteo polyosoma exsul Buteo polyosoma poecilochrous Buteo poecilochrous Buteo polyosoma polyosoma Buteo polyosoma polyosoma Buteo refectus Buteo buteo refectus Buteogallus urubitinga urubitinga Buteogallus urubitinga urubitinga Bycanistes Ceratogymna Cabalus modestus Cabalus modestus Extinct Cacatua roseicapilla Eolophus roseicapillus Cacicus holosericeus Amblycercus holosericus Calopelia puella brehmeri Turtur brehmeri Canachites franklinii Canachites canadensis Carduelis carduelis caniceps Carduelis carduelis caniceps Carduelis carduelis parva Carduelis carduelis parva Carduelis magellanicus Carduelis magellanica Carduelis psaltria colombiana Carduelis psaltria colombiana

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Carduelis psaltria hesperofila Carduelis psaltria hesperofila Caryothaustes humeralis Parkerthraustes humeralis Casuarius aruensis Casuarius casuarius aruensis Catharacta skua hamiltoni Catharacta skua hamiltoni Cathayornis Cathayornis Extinct Cathayornis yandica Cathayornis yandica Extinct minimus Centrocercus minimus Extinct Ceranopterus Ceranopterus Certhidea fusca Certhidea olivacea fusca Ceryle maxima Megaceryle maxima Ceyx melanurus melanurus Ceyx melanurus melanurus Ceyx melanurus mindanensis Ceyx melanurus mindanensis Ceyx melanurus samarensis Ceyx melanurus samarensis Ceyx rufidorsum Ceyx rufidorsa = Ceyx erithaca Changchengornis Changchengornis Extinct Chaoyangia Extinct Charadrius venustus Charadrius pallidus Chelychelynechen quassus Chelychelynechen quassus Extinct Chenonetta finschi Chenonetta finschi Extinct Chlamydotis houbara Chlamydotis undulata Chlamydotis macqueenii Chlamydotis macqueenii Chlamydotis undulata fuerteventurae Chlamydotis undulata fuerteventurae Chloridops regiskongi Chloridops regiskongi Extinct Chloridops wahi Chloridops wahi Extinct Chloris chloris Carduelis chloris Chloris sinica Carduelis sinica Chloris spinoides Carduelis spinoides Chlorophoneus dohertyi Telophorus dohertyi Chlorophoneus nigrifrons Telophorus nigrifrons Chlorophoneus sulfureopectus Telophorus sulfureopectus Choreotis australis Ardeotis australis Choriotis Ardeotis Chroicocephalus cirrocephalus Larus cirrocephalus Chroicocephalus genei Larus genei Chroicocephalus philadelphia Larus philadelphia Chroicocephalus ridibundus Larus ridibundus Chroicocephalus scopulinus Larus scopulinus Chroicocephalus serranus Larus serranus Chrysomus icterocephalus Agelaius icterocephalus Chrysomus ruficapillus Agelaius ruficapillus Ciconia alba Ciconia ciconia alba Cinclodes aricomae Cinclodes aricomae Cinclosoma alisteri Cinclosoma cinnamomeum alisteri Cinclosoma marginatum Cinclosoma castaneothorax marginatum Cissopsis Cissopis Extinct Clamator cafer Clamator levaillantii Clamator levaillantii Clamator levaillantii Cnemiornis Cnemiornis Extinct Cnemiornis calcitrans Cnemiornis calcitrans Extinct Cnemiornis gracilis Cnemiornis gracilis Extinct

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Coccothraustes melanozanthos Mycerobas melanozanthos Coccothraustes vespertinus brooksi Coccothraustes vespertinus Coccothraustes vespertinus Coccothraustes vespertinus vespertinus Coccycua Piaya Collocalia esculenta becki Collocalia esculenta becki Collocalia esculenta cyanoptila Collocalia esculenta cyanoptila Collocalia esculenta nitens Collocalia esculenta nitens Collocalia salangana Aerodramus salanganus Collocalia vanikorensis Aerodramus vanikorensis Columba albilinea Columba fasciata Columba rufina Columba cayennensis Columbigallina minuta Columbina minuta Columbigallina passerina Columbina passerina Columbigallina talpacoti Columbina talpacoti Compsohalieus fuscescens Phalacrocorax fuscescens Compsohalieus harrisi Phalacrocorax harrisi Compsohalieus neglectus Phalacrocorax neglectus Compsohalieus penicillatus Phalacrocorax penicillatus Compsohalieus perspicillatus Phalacrocorax perspicillatus Concornis Concornis Extinct Concornis lacustris Concornis lacustris Extinct Confuciusornis Confuciusornis Extinct Confuciusornis sanctus Confuciusornis sanctus Extinct Conirostrum cinereum fraseri Conirostrum cinereum fraseri Copepteryx hexeris Copepteryx hexeris Extinct Corythospis Corythopis Extinct Cosmopelia elegans Phaps elegans Cossyphicula roberti Cossypha roberti Coturnix coturnix japonica Coturnix japonica Crex albicollis Porzana albicollis concolor Corythaixoides concolor Crinifer leucogaster Corythaixoides leucogaster Crinifer personatus Corythaixoides personatus Crithagra albogularis Serinus albogularis Crithagra buchanani Serinus buchanani Crithagra sulphurata Serinus sulphuratus Cyanoramphus erythrotis Cyanoramphus erythrotis Cyclarhis gujanensis contrerasi Cyclarhis gujanensis contrerasi Cyclarhis gujanensis dorsalis Cyclarhis gujanensis dorsalis Cygnus bewickii Cygnus columbianus Dasylophus Phaenicophaeus franklinii Dendragapus canadensis Dendragapus fuliginosus Dendragapus obscurus Dendrocolaptes concolor Dendrocolaptes certhia concolor Dendrocopos leucotos leucotos Dendrocopos leucotos leucotos Dendrocopos leucotos lilfordi Dendrocopos leucotos lilfordi Dendrocopos leucotos subcirris Dendrocopos leucotos subcirris Dendrocopos major brevirostris Dendrocopos major brevirostris Dendrocopos major japonicus Dendrocopos major japonicus Dendrocopos major pinetorum Dendrocopos major pinetorum

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Dendroica auduboni Dendroica coronata auduboni Dendroica nigrescens halseii Dendroica nigrescens halseii Dendroica nigrescens nigrescens Dendroica nigrescens nigrescens Dendrospiza capistrata Serinus capistratus Dendrospiza hyposticta Serinus hypostictus Dendrospiza koliensis Serinus koliensis Dendrospiza scotops Serinus scotops Diglossa carbonaria brunneiventris Diglossa brunneiventris Diglossa carbonaria carbonaria Diglossa carbonaria carbonaria Diglossa carbonaria gloriosa Diglossa gloriosa Diglossa gloriosissima boylei Diglossa gloriosissima boylei Diglossa gloriosissima gloriosissima Diglossa gloriosissima gloriosissima Diglossa humeralis aterrima Diglossa humeralis aterrima Diglossa humeralis humeralis Diglossa humeralis humeralis Diglossa humeralis nocticolor Diglossa humeralis nocticolor Diglossa mystacalis albilinea Diglossa mystacalis albilinea Diglossa mystacalis mystacalis Diglossa mystacalis mystacalis Diglossa mystacalis pectoralis Diglossa mystacalis pectoralis Diglossa mystacalis unicincta Diglossa mystacalis unicincta Dinornis maximus Dinornis novaezealandiae Dinornis robustus Dinornis giganteus Dinornis struthoides Dinornis novaezealandiae Diomedea bassi Thalassarche chlororhynchos bassi Diomedea exulans dabbenena Diomedea exulans dabbenena Diopsittaca nobilis Ara nobilis Dixiphia pipra Pipra pipra Drepanornis albertisi Epimachus albertisi Dromiceius novaehollandiae Dromaius novaehollandiae Dyaphorophyia chalybea Platysteira chalybea Emblema bella Stagonopleura bella Emblema guttata Stagonopleura guttata Emeus huttonii Emeus crassus Enantiornis leali Enantiornis leali Eoalulavis Eoalulavis Extinct Eocoracias brachyptera Eocoracias brachyptera Extinct Eocypselus vincenti Eocypselus vincenti Extinct Eoglaucidium pallas Eoglaucidium pallas Extinct Eogrus aeola Eogrus aeola Extinct capito capito Eopsaltria leucops Tregellasia leucops Ephippiorhynchus senegalis Ephippiorhynchus senegalensis Eriocnemis sapphiropygia Eriocnemis luciani sapphiropygia Erythrina mexicana Carpodacus mexicanus Erythropygia Cercotrichas Euaegotheles tatei Euaegotheles tatei Euaegotheles tatei Euaegotheles tatei Eudromia elegans albida Eudromia elegans albida Eudromius morinellus Charadrius morinellus Eudyptes chrysocome chrysocome Eudyptes chrysocome chrysocome Eudyptes chrysocome moseleyi Eudyptes chrysocome moseleyi Eudyptes chrysocome moseleyi Eudyptes chrysocome moseleyi

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Eulabeornis cajanea Aramides cajanea Euleucocarbo chalconotus Phalacrocorax chalconotus Euleucocarbo colensoi Phalacrocorax colensoi Euleucocarbo onslowi Phalacrocorax onslowi Euleucocarbo ranfuriyi Phalacrocorax ranfuriyi Euodice cantans Lonchura cantans Euphagus carolinensis Euphagus carolinus Euplectus hordeacea Euplectes hordeaceus Euryanas finschi Chenonetta finschi Euryapteryx exilis Euryapteryx curtus Extinct Euryapteryx geranoides Euryapteryx geranoides Extinct sinensis/chinensis Coturnix chinensis Falco peregrinus calidus Falco peregrinus calidus Falco peregrinus peregrinus Falco peregrinus peregrinus Finschia novaeseelandiae Mohoua novaeseelandiae Fluvicola Fluvicola Fluvicola pica albiventer Fluvicola pica albiventer Francolinus ochropectus ochropectus Fringilla coelebs coelebs Fringilla coelebs coelebs Fulica chathamensis chathamensis Fulica chathamensis chathamensis Fulica chathamensis prisca Fulica chathamensis prisca Gallinula martinica Porphyrio martinica Gallinuloides wyomingensis Gallinuloides wyomingensis Extinct Garritornis isidorei Pomatostomus isidorei Geobates crassirostris Geositta crassirostris Geobiastes Brachypteracias Geobiastes squamigera Brachypteracias squamigera Extinct Geochen rhuax Geochen rhuax Geokichla princei Zoothera princei Geranopterus alatus Geranopterus alatus Extinct Geranopterus milneedwardsi Geranopterus milneedwardsi Extinct Gobipteryx minuta Gobipteryx minuta Extinct Guarouba guarouba Aratinga guarouba Gyalophylax hellmayri Synallaxis hellmayri Gymnogyps kofordi Gymnogyps kofordi Extinct Gypopsitta aurantiocephala Gypopsitta aurantiocephala Extinct Gypopsitta coccinicollaris Gypopsitta coccinicollaris Haematopus frazari Haematopus palliatus frazari Hagedashia hagedash Bostrychia hagedash Halcyon leucopygia Todirhamphus leucopygius Halcyon macleayii Todirhamphus macleayii Halcyon sancta Todirhamphus sanctus Halcyon winchelli Todirhamphus winchelli Halietor pygmaeus Phalacrocorax pygmeus Haplochelidon andecola Hirundo andecola Hemignathus flava/flavus Hemignathus chloris Hemignathus flavus Hemignathus chloris Hemignathus lucidus affinis Hemignathus lucidus affinis Hemignathus lucidus hanapepe Hemignathus lucidus hanapepe Hemignathus lucidus lucidus Hemignathus lucidus lucidus Hemignathus stejnegeri Hemignathus stejnegeri Extinct

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Hemignathus virens chloris Hemignathus virens chloris Hemignathus virens stejnegeri Hemignathus virens stejnegeri Hemignathus virens virens Hemignathus virens virens Hemignathus virens wilsoni Hemignathus virens wilsoni Hemimacronyx chloris Anthus chloris Hesperornis regalis Hesperornis regalis Extinct Heterocnus Tigrisoma Hieraaetus fasciatus fasciatus Hieraaetus fasciatus fasciatus Hieraaetus fasciatus spilogaster Hieraaetus spilogaster Hieraaetus morphnoides morphnoides Hieraaetus morphnoides morphnoides Hieraaetus morphnoides weiskei Hieraaetus morphnoides weiskei Hieraaetus wahlbergi Aquila wahlbergi Himatione sanguinea sanguinea Himatione sanguinea sanguinea Hippolais caligata caligata Hippolais caligata caligata Hippolais caligata rama Hippolais rama Hippolais pallida elaeica Hippolais pallida elaeica Hydranassa caerula Egretta caerula Hydranassa novaehollandiae Egretta novaehollandiae Hydrocoleus minutus Larus minutus Hylopsar Lamprotornis Hypoleucos auritus Phalacrocorax auritus Hypoleucos olivaceus Phalacrocorax olivaceus Hypoleucos sulcirostris Phalacrocorax sulcirostris Hypoleucos varius Phalacrocorax varius Iberomesornis romerali Iberomesornis romerali Extinct Ibycter americanus Ibycter americanus Ichthyornis antecessor Ichthyornis antecessor Extinct Ichthyornis dispar Ichthyornis dispar Extinct Icterus cayanensis cayanensis Icterus cayanensis cayanensis Icterus cayanensis periporphyrus Icterus cayanensis periporphyrus Icterus galbula abeillei Icterus galbula abeillei Icterus jamacaii croconotus Icterus jamacaii croconotus Icterus leucopteryx leucopteryx Icterus leucopteryx leucopteryx Icterus mesomelas taczanowskii Icterus mesomelas taczanowskii Icterus nigrogularis nigrogularis Icterus nigrogularis nigrogularis Icterus spurius spurius Icterus spurius spurius Idioptilon Hemitriccus Jeholornis prima Jeholornis prima Extinct Jungornis tesselatus Jungornis tesselatus Extinct scoticus Lagopus lagopus Laputa robusta Laputa robusta Extinct Larus cirrocephalus poicephalus Larus cirrocephalus poicephalus Larus kumlieni Larus glaucoides kumlieni Larus novaehollandiae scopulinus Larus novaehollandiae scopulinus Larus smithsonianus Larus argentatus smithsonianus Lectavis bretincola Lectavis bretincola Extinct Lepidogrammus Phaenicophaeus Lepidothrix suavissima Pipra suavissima Leptopterus madagascarinus Cyanolanius madagascarinus Leptopterus viridis Artamella viridis Leucocarbo bougainvilli Phalacrocorax bougainvilli

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Leucocarbo capensis Phalacrocorax capensis Leucocarbo nigrogularis Phalacrocorax nigrogularis Leucophaeus scoresbii Larus scoresbii Leucosticte arctoa littoralis Leucosticte tephrocotis littoralis Leucosticte littoralis Leucosticte tephrocotis littoralis Leucotreron cincta Ptilinopus cinctus Leucotreron subgularis Ptilinopus subgularis Liaoningornis Liaoningornis Extinct Limenavis patagonica Limenavis patagonica Extinct Limnoctites rectirostris Hylocryptus rectirostris Linaria cannabina Carduelis cannabina Lithoptila abdounensis Lithoptila abdounensis Extinct Lithornis celetius Lithornis celetius Extinct Lithornis plebius Lithornis plebius Extinct Lithornis promiscuus Lithornis promiscuus Extinct Lonchura cucullata cucullata Lonchura cucullata cucullata Lonchura malacca atricapilla Lonchura malacca atricapilla Lonchura pectoralis Heteromunia pectoralis Lophophaps plumifera Geophaps plumifera Lothyra nycthera Lothura nycthemera Loxops coccineus caeruleirostris Loxops caeruleirostris Loxops parvus Hemignathus parvus Loxops sagittirostris Hemignathus sagittirostris Loxops virens Hemignathus virens Loxops/Akialoa stejnegeri Hemignathus stejnegeri Lyrurus mlokosiewiczi Tetrao mlokosiewiczi Lyrurus tetrix Tetrao tetrix Malurus assimilis Malurus lamberti assimilis Malurus dulcis Malurus lamberti dulcis Malurus leuconotus Malurus leucopterus leuconotus Malurus rogersi Malurus lamberti rogersi Megabyas flammulatus Bias flammulatus Megalapteryx benhami Megalapteryx benhami Extinct Megaloprepria magnifica Ptilinopus magnificus Megapodius duperryi Megapodius freycinet duperryi Melaenornis pallidus Melaenornis pallidus Melaenornis silens Sigelus silens Melanitta americana Melanitta americana Melanochlora sultanea gayeti Melanochlora sultanea gayeti Melanochlora sultanea sultanea Melanochlora sultanea sultanea Meliphaga penicillata Lichenostomus penicillatus Messelastur gratulator Messelastur gratulator Extinct Microcarbo africanus Phalacrocorax africanus Microcarbo coronatus Phalacrocorax coronatus Microcarbo melanoleucos Phalacrocorax melanoleucos Microcarbo niger Phalacrocorax niger Microcarbo pygmaeus Phalacrocorax pygmaeus leucophaea Microeca fascinans Micropalama himantopus Calidris himantopus Miliaria calandra calandra Miliaria calandra calandra Misocalius Chalcites

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Misocalius osculans Chrysococcyx osculans Monticola bensoni Pseudocossyphus bensoni Monticola erythronota Monticola erythronotus Motacilla baicalensis Motacilla alba baicalensis Motacilla leucopsis Motacilla alba leucopsis Motacilla lugens Motacilla alba lugens Motacilla ocularis Motacilla alba ocularis Myiarchus swainsoni swainsoni Myiarchus swainsoni swainsoni Myiarchus tuberculifer atriceps Myiarchus tuberculifer atriceps Myiarchus tuberculifer nigricapillus Myiarchus tuberculifer nigricapillus Myiarchus tuberculifer platyrhynchus Myiarchus tuberculifer platyrhynchus Myiarchus tyrannulus bahiae Myiarchus tyrannulus bahiae Myiarchus tyrannulus insularum Myiarchus tyrannulus insularum Myiobius sulphureipygius Myiobius barbatus sulphureipygius Nannopterum harrisi Phalacrocorax harrisi Nannus troglodytes Troglodytes troglodytes Nectarinia humbloti humbloti Nectarinia humbloti humbloti Nectarinia humbloti mohelica Nectarinia humbloti mohelica Nectarinia notata moebii Nectarinia notata moebii Nectarinia notata notata Nectarinia notata notata Nectarinia notata voeltzkowi Nectarinia notata voeltzkowi Nectarinia souimanga abbotti Nectarinia sovimanga abbotti Nectarinia souimanga aldabrensis Nectarinia sovimanga aldabrensis Nectarinia souimanga buchenorum Nectarinia sovimanga buchenorum Nectarinia souimanga comorensis Nectarinia sovimanga comorensis Nectarinia souimanga souimanga Nectarinia sovimanga souimanga Nesocarbo campbelli Phalacrocorax campbelli Neuquenornis volans Neuquenornis volans Extinct Ninox sumbaensis Ninox sumbaensis Extinct Noguerornis Noguerornis Notocarbo atriceps Phalacrocorax atriceps Notocarbo bransfieldensis Phalacrocorax bransfieldensis Notocarbo georgianus Phalacrocorax georgianus Notocarbo verrucosus Phalacrocorax verrucosus Nyctiornis amicta Nyctyornis amictus Oceanitidae Hydrobatidae Ochetorhynchus certhioides Upucerthia certhioides Ochraspiza reichenowi Serinus reichenowi Ochrospiza atrogularis Serinus atrogularis Ochrospiza dorsostriata Serinus dorsostriatus Ochrospiza leucopygia Serinus leucopygius Ochrospiza mozambica Serinus mozambicus Ochrospiza xanthopygia Serinus xanthopygius Ochthoeca pulchella Silvicultrix pulchella Odontopteryx toliapica Odontopteryx toliapica Extinct Odontospiza caniceps Lonchura griseicapilla Oreopeleia Geotrygon Oreopelia chrysia Geotrygon chrysia Oreophylax moreirae Schizoeaca moreirae Orthiospiza howarthi Orthiospiza howarthi Extinct Orthonyx dorsalis Orthonyx temminckii dorsalis

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Orthonyx novaeguineae Orthonyx temminckii novaeguineae Orthonyx victoriana Orthonyx temminckii victoriana Orthopsittaca manilata Ara manilata Ortygospiza atricapilla Ortygospiza atricollis Pachyornis australis Pachyornis australis Extinct Pachyornis mappini Pachyornis mappini Extinct Palaeotis Palaeotis Extinct Paraortygoides messelensis Paraortygoides messelensis Extinct Paraortygoides radagasti Paraortygoides radagasti Extinct Paraprefica kelleri Paraprefica kelleri Extinct Pareudiastes pacificus Pareudiastes pacificus Extinct Pareudiastes sylvestris Edithornis sylvestris Parisoma layardi Sylvia layardi Parus bicolor atricristatus Parus atricristatus Parus bicolor bicolor Parus bicolor bicolor Parus dichrous Lophophanes dichrous Parus niger niger Parus niger niger Parus rubidiventris Periparus rubidiventris Parus venustulus Periparus venustulus Passer ammodendri ammodendri Passer ammodendri ammodendri Passer griseus griseus Passer griseus griseus Passer hispaniolensis hispaniolensis Passer hispaniolensis hispaniolensis Passer melanurus melanurus Passer melanurus melanurus Passer rutilans rutilans Passer rutilans rutilans Passerella megarhyncha Passerella iliaca megarhyncha Passerella schistacea Passerella iliaca schistacea Passerella unalaschcensis Passerella iliaca unalaschcensis Patagioenas fasciata Columba fasciata Patagioenas plumbea Columba plumbea Patagioenas speciosa Columba speciosa Patagioenas subvinacea Columba subvinacea Patagopteryx deferrariisi Patagopteryx deferrariisi Extinct Pedionomus Pedionomus Pelagornis Extinct Pelecanus roseus Pelecanus onocrotalus roseus Penthoceryx Cacomantis Periparus ater ater Periparus ater ater Periparus elegans elegans Periparus elegans elegans Periparus elegans mindanensis Periparus elegans mindanensis cucullata cucullata Petronia petronia petronia Petronia petronia petronia Petrophasa blaauwi Geophaps smithii blaauwi Petrophasa ferruginea Petrophassa plumifera ferruginea Petrophasa peninsulae Petrophassa scripta Pezoporus wallicus wallicus Pezoporus wallicus wallicus Phacellodomus maculipectus Phacellodomus striaticollis maculipectus Pholia Cinnyricinclus Phylloscopus abietinus Phylloscopus collybita abietinus Phylloscopus bonelli orientalis Phylloscopus bonelli orientalis Phylloscopus borealis kennecotti Phylloscopus borealis kennecotti

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Phylloscopus borealis xanthodryas Phylloscopus borealis xanthodryas Phylloscopus cantator cantator Phylloscopus cantator cantator Phylloscopus collybita abietinus Phylloscopus collybita abietinus Phylloscopus collybita abietinus Phylloscopus collybita abietinus Phylloscopus collybita brevirostris Phylloscopus collybita brevirostris Phylloscopus collybita caucasicus Phylloscopus collybita caucasicus Phylloscopus collybita tristis Phylloscopus collybita tristis Phylloscopus davisoni davisoni Phylloscopus davisoni davisoni Phylloscopus davisoni disturbans Phylloscopus davisoni disturbans Phylloscopus davisoni klossi Phylloscopus davisoni klossi Phylloscopus davisoni ogilviegranti Phylloscopus davisoni ogilviegranti Phylloscopus emeiensis Phylloscopus emeiensis Phylloscopus hainanus Phylloscopus hainanus Phylloscopus inornatus humei Phylloscopus inornatus humei Phylloscopus kansuensis Phylloscopus proregulus kansuensis Phylloscopus mackensianus Phylloscopus umbrovirens mackensianus Phylloscopus maculipennis Phylloscopus maculipennis maculipennis maculipennis Phylloscopus minullus Phylloscopus ruficapillus minullus Phylloscopus orientalis Phylloscopus orientalis Phylloscopus poliocephalus Phylloscopus poliocephalus giulianettii giulianettii Phylloscopus presbytes floris Phylloscopus presbytes floris Phylloscopus reguloides assamensis Phylloscopus reguloides assamensis Phylloscopus reguloides claudiae Phylloscopus reguloides claudiae Phylloscopus reguloides fokiensis Phylloscopus reguloides fokiensis Phylloscopus reguloides goodsoni Phylloscopus reguloides goodsoni Phylloscopus reguloides kashmiriensis Phylloscopus reguloides kashmiriensis Phylloscopus reguloides reguloides Phylloscopus reguloides reguloides Phylloscopus reguloides ticehursti Phylloscopus reguloides ticehursti Phylloscopus ruficapilla minullus Phylloscopus ruficapillus minullus Phylloscopus sarasinorum sarasinorum Phylloscopus sarasinorum sarasinorum Phylloscopus sindianus lorenzii Phylloscopus sindianus lorenzii Phylloscopus sindianus sindianus Phylloscopus sindianus sindianus Phylloscopus trivirgatus benguetensis Phylloscopus trivirgatus benguetensis Phylloscopus trivirgatus trivirgatus Phylloscopus trivirgatus trivirgatus Phylloscopus trochiloides viridianus Phylloscopus trochiloides viridianus Phylloscopus trochilus trochilus Phylloscopus trochilus trochilus Phylloscopus umbrovirens Phylloscopus umbrovirens fugglescouchmani fugglescouchmani Phylloscopus yunnanensis Phylloscopus yunnanensis Pica pica camtschatica Pica pica camtschatica Pica pica sericea Pica pica sericea Picoides kizuki Dendrocopos kizuki Picoides tridactylus alpinus Picoides tridactylus alpinus Picus canus canus Picus canus canus Picus canus jessoensis Picus canus jessoensis Picus viridis viridis Picus viridis viridis Pionopsitta coccinicollaris Pionopsitta haematotis coccinicollaris Pionopsitta vulturina Gypopsitta vulturina Piranga erythrocephala canida Piranga erythrocephala canida

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Piranga flava lutea Piranga flava lutea Piranga flava rosacea Piranga flava rosacea Piranga flava testacea Piranga flava testacea Piranga leucoptera ardens Piranga leucoptera ardens Piranga leucoptera leucoptera Piranga leucoptera leucoptera Pitylus grossus Saltator grossus Platycercus adscitus adsiticus Platycercus adscitus adsiticus Platycercus adscitus amathusiae Platycercus adscitus amathusiae Platycercus adscitus mackaiensis Platycercus adscitus mackaiensis Platycercus adscitus palliceps Platycercus adscitus palliceps Platycercus elegans adelaidae Platycercus elegans adelaidae Platycercus elegans elegans Platycercus elegans elegans Platycercus elegans flaveolus Platycercus elegans flaveolus Platycercus elegans nigrescens Platycercus elegans nigrescens Platycercus eximius diemenensis Platycercus eximius diemenensis Platycercus eximius eximius Platycercus eximius eximius Platycercus icterotis xanthogenys Platycercus icterotis xanthogenys Poecile carolinensis carolinensis Poecile carolinensis carolinensis Poecile montanus borealis Poecile montanus borealis Poecile montanus songarus Poecile montanus songarus Poecile palustris brevirostris Poecile palustris brevirostris Poecile palustris palustris Poecile palustris palustris Poecile varius Parus varius Poecilurus candei Synallaxis candei Poecilurus scutatus Synallaxis scutatus Poephila annulosa Taeniopygia bichenovii annulosa Poephila atropygialis Poephila cincta atropygialis Poephila bichenovii Taeniopygia bichenovii Poephila castanotis Taeniopygia guttata castanotis Poephila guttata Taeniopygia guttata Poephila guttata Taeniopygia guttata Poephila hecki Poephila acuticauda hecki Poephila leucotis Poephila personata leucotis Pogonotriccus orbitalis orbitalis Poliolimnas flaviventer Porzana flaviventer Poliospiza burtoni Serinus burtoni Poliospiza gularis Serinus gularis Poliospiza leucoptera Serinus leucopterus Poliospiza mennelli Serinus mennelli Poliospiza striolata Serinus striolatus Poliospiza tristriata Serinus tristriatus Polyplancta aurescens Heliodoxa aurescens Porphyrio hochstetteri Porphyrio mantelli Porphyrio poliocephalus Porphyrio porphyrio poliocephalus Porphyrio porphyrio madagascariensis Porphyrio porphyrio madagascariensis Porphyrio porphyrio melanotus Porphyrio porphyrio melanotus Porphyrio porphyrio pulverulentus Porphyrio porphyrio pulverulentus Porphyrio porphyrio seistanicus Porphyrio porphyrio seistanicus Porphyrio pulverulentus Porphyrio porphyrio Porzana erythrops Neocrex erythrops Porzana flavirostra Amaurornis flavirostra

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Porzana olivieri Amaurornis olivieri Prefica nivea Prefica nivea Extinct Presbyornis pervetus Presbyornis pervetus Extinct Primapus lacki Primapus lacki Extinct Primobucco mcgrewi Primobucco mcgrewi Extinct Primolius auricollis Ara auricollis Primolius couloni Ara couloni Primozygodactylus danielsi Primozygodactylus danielsi Extinct Procarduelis vinacea Carpodacus vinaceus Prophaethon shrubsolei Prophaethon shrubsolei Extinct Protocypselomorphus manfredkelleri Protocypselomorphus manfredkelleri Extinct Psarocolius latirostris Ocyalus latirostris Psarocolius yuracares Gymnostinops yuracares Pseudoalcippe abyssinica Illadopsis abyssinica Pseudobulweria rostrata rostrata Pseudobulweria rostrata rostrata Pseudobulweria rostrata trouessarti Pseudobulweria rostrata trouessarti Pseudochloroptila totta Serinus totta Pseudoseisuropsis cuelloi Pseudoseisuropsis cuelloi Extinct Pseudoseisuropsis nehuen Pseudoseisuropsis nehuen Extinct Psittacopes lepidus Psittacopes lepidus Extinct Psittacula cyanocephala roseus Psittacula cyanocephala Psittacula krameri borelis Psittacula krameri borelis Psittacula krameri krameri Psittacula krameri krameri Psittacula krameri manillensis Psittacula krameri manillensis Psophodes lateralis Psophodes olivaceus Psophodes leucogaster Psophodes nigrogularis Pterodroma deserta Pterodroma feae deserta Pteroglossus flavirostris Pteroglossus azara flavirostris Pteroglossus humboldti Pteroglossus inscriptus humboldti Pteroglossus reichenowi Pteroglossus bitorquatus reichenowi Pteroglossus sturmii Pteroglossus bitorquatus sturmii Ptilolaemus Ptilolaemus Ptiloris alberti Ptiloris magnificus alberti Puffinus bailloni Puffinus lherminieri bailloni Puffinus baroli Puffinus assimilis baroli Puffinus boydi Puffinus assimilis boydi Puffinus colstoni Puffinus lherminieri colstoni Puffinus dichrous Puffinus lherminieri dichrous Puffinus elegans Puffinus assimilis elegans Puffinus haurakiensis Puffinus assimilis haurakiensis Puffinus kermadecensis Puffinus assimilis kermadecensis Puffinus loyemilleri Puffinus lherminieri loyemilleri Puffinus myrtae Puffinus assimilis myrtae Puffinus nicolae Puffinus lherminieri nicolae Puffinus polynesiae Puffinus lherminieri polynesiae Puffinus puffinus mauretanicus Puffinus mauretanicus Puffinus puffinus yelkouan Puffinus yelkouan Puffinus subalaris Puffinus lherminieri subalaris Puffinus temptator Puffinus lherminieri temptator Puffinus tunneyi Puffinus assimilis tunneyi Pulchrapollia gracilis Pulchrapollia gracilis Extinct

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Purpureicephalus haematonotus Purpureicephalus haematonotus Pyrrhula pyrrhula iberiae Pyrrhula pyrrhula iberiae Quercypsitta ivani Quercypsitta ivani Extinct Quercypsitta sudrei Quercypsitta sudrei Extinct Quiscalus versicolor Quiscalus quiscula versicolor Rahona Rahonavis Extinct Rahonavis ostromi Rahonavis ostromi Extinct Rallina amauroptera Rallina eurizonoides amauroptera Rallina castaneiceps Anurolimnas castaneiceps aquaticus aquaticus Rallus aquaticus aquaticus Rallus modestus Rallus modestus Rallus philippensis dieffenbachii Rallus philippensis dieffenbachii Rallus sylvestris Gallirallus sylvestris Ramphastos ariel Ramphastos vitellinus Ramphastos sulfuratus brevicarinatus Ramphastos sulfuratus brevicarinatus Ramphastos sulfuratus sulfuratus Ramphastos sulfuratus sulfuratus Ramphastos tucanus cuvieri Ramphastos tucanus cuvieri Ramphastos tucanus tucanus Ramphastos tucanus tucanus Ramphastos vitellinus ariel Ramphastos vitellinus ariel Ramphastos vitellinus vitellinus Ramphastos vitellinus vitellinus Reinarda squamata Tachornis squamata Rhamphococcyx Phaenicophaeus Rhamphococcyx calyorhynchus Zanclostomus calyorhynchus Rhinoplax Ptilolaemus Rhinortha Phaenicophaeus Rhopodytes Phaenicophaeus Rhynchotus rufescens macullicollis Rhynchotus rufescens maculicollis Rhynchotus rufescens pallescens Rhynchotus rufescens pallescens Rhynoptynx Pseudoscops Sandcoleus copiosus Sandcoleus copiosus Extinct Sapeornis chaoyangensis Sapeornis chaoyangensis Extinct Scaniacypselus szarskii Scaniacypselus szarskii Extinct Scaniacypselus wardi Scaniacypselus wardi Extinct Scenopoeetes dentirostris Ailuroedus dentirostris Schistes geoffroyi Schistes geoffroyi Schistocichla leucostigma Percnostola leucostigma Scytalopus magellanicus simonsi Scytalopus simonsi Scytalopus unicolor parvirostris Scytalopus parvirostris Scythops Scythrops Extinct Seicercus affinis intermedius Seicercus affinis intermedius Seicercus affinis ocularis Seicercus affinis ocularis Seicercus castaniceps castaniceps Seicercus castaniceps castaniceps Seicercus cognitus Seicercus affinis intermedius Seicercus omeiensis Seicercus omeiensis Seicercus soror Seicercus soror Seicercus tephrocephalus Seicercus tephrocephalus Seicercus valentini Seicercus valentini Seicercus whistleri whistleri Seicercus whistleri whistleri Seicercus xanthoschistos tephrodiras Seicercus xanthoschistos tephrodiras Seicercus xanthoschistos Seicercus xanthoschistos xanthoschistos xanthoschistos

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Selenidera langsdorffii Selenidera reinwardtii langsdorffii Semeiophorus Macrodipteryx Sericornis citreogularis cairnsi Sericornis citreogularis cairnsi Sericornis citreogularis citreogularis Sericornis citreogularis citreogularis Sericornis magnirostris magnirostris Sericornis magnirostris magnirostris Sericornis magnirostris viridior Sericornis magnirostris viridior Serinops Serinus Serinus canicollis canicollis Serinus canicollis canicollis Serinus canicollis flavivertex Serinus canicollis flavivertex Sicalis flaveola pelzelni Sicalis flaveola pelzelni Sinornis santensis Sinornis santensis Somateria borealis Somateria mollissima borealis Somateria dresseri Somateria mollissima dresseri Somateria v-nigrum Somateria mollissima v-nigrum Soroavisaurus australis Soroavisaurus australis Extinct Spermestes bicolor Lonchura bicolor Spermestes cucullatus Lonchura cucullatus=Lonchura cucullata Spermestes cucullatus Lonchura cucullata Spermestes fringilloides Lonchura fringilloides Sphecotheres flaviventris Sphecotheres flaviventris Sphecotheres vieilloti Sphecotheres vieilloti Sphenoeacus mentalis Melocichla mentalis Sphenurus oxyura Treron oxyura Spilaeornis Spilornis Spindalis portoricensis Spindalis zena portoricensis Spinus barbatus Carduelis barbata Spinus cucullatus Carduelis cucullata Spizaetus pinskeri Spizaetus philippensis pinskeri Steganopus tricolor Phalaropus tricolor Stercorarius maccormicki Catharacta maccormicki Sterna nigra Chlidonias niger Sterna sandvicensis acuflavida Sterna sandvicensis acuflavida Sterna sandvicensis eurygnatha Sterna sandvicensis eurygnatha Stictocarbo aristotelis Phalacrocorax aristotelis Stictocarbo featherstoni Phalacrocorax featherstoni Stictocarbo gaimardi Phalacrocorax gaimardi Stictocarbo magellanicus Phalacrocorax magellanicus Stictocarbo pelagicus Phalacrocorax pelagicus Stictocarbo urile Phalacrocorax urile Stigmatopelia senegalensis Streptopelia senegalensis Stipiturus westernensis Stipiturus malachurus Sylphornis bretouensis Sylphornis bretouensis Extinct Sylvia abyssinica Illadopsis abyssinica Sylvia Sylvia sarda balearica Sylvia crassirostris Sylvia hortensis crassirostris Synallaxis chinchipensis Synallaxis stictothorax chinchipensis Synallaxis gularis Hellmayrea gularis Synoicus Coturnix Synthliboramphus hypoleucus scrippsi Synthliboramphus hypoleucus scrippsi soemmerringii scintillans Syrmaticus soemmerringii scintillans

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Taeniopygia bichenovii annulosa Taeniopygia bichenovii annulosa Tangara pulcherrima Iridophanes pulcherrima corythaix livingstonii Tauraco livingstonii Tauraco corythaix persa Tauraco persa Tauraco corythaix schalowi Tauraco schalowi Tauraco porphyreolophus Gallirex porphyreolophus Telespiza cantans cantans Telespiza cantans cantans Telespiza persecutrix Telespiza persecutrix Extinct Telespiza ypsilon Telespiza ypsilon Extinct Teratornis merriami Teratornis merriami Extinct Thalassarche bassi Thalassarche chlororhyncos bassi Thalasseus bergii Sterna bergii Thambetochen xanion Thambetochen xanion Extinct Tinamus tao kleei Tinamus tao kleei Tonsala hildegardae Tonsala hildegardae Extinct Totanus ?Tringa? Tregellasia albigularis Tregellasia leucops albigularis Tregellasia nana Tregellasia capito nana Trichastoma malaccense Malacocincla malaccensis Tumbezia salvini Ochthoeca salvini Turdus dauma Zoothera dauma Tympanistria tympanistria Turtur tympanistria pinnatus Tympanuchus cupido Tynskya eocaena Tynskya eocaena Extinct Tyranniscus Zimmerius Tyto pratincola Tyto alba pratincola Vangulifer mirandus Vangulifer mirandus Extinct Vangulifer neophasis Vangulifer neophasis Extinct Vegavis iaai Vegavis iaai Extinct Vireo olivaceus chivi Vireo olivaceus chivi Vireo olivaceus diversus Vireo olivaceus diversus Vireo olivaceus olivaceus Vireo olivaceus olivaceus Vireo olivaceus solimoensis Vireo olivaceus solimoensis Vireolanius leucotis simplex Vireolanius leucotis simplex Viridonia virens Hemignathus virens Vorona berivotrensis Vorona berivotrensis Extinct Xenopipo holochlora Xenopipo holochlora Xenopipo unicolor Xenopipo unicolor Xenopipo uniformis Xenopipo uniformis Xestospiza conica Xestospiza conica Extinct Xestospiza fastigialis Xestospiza fastigialis Extinct Yungavolucris brevipedalis Yungavolucris brevipedalis Extinct Zanclostomus Zanclostomus Extinct Zosterops conspicillatus rotensis Zosterops rotensis

152 APPENDIX B: SOURCES FOR CHAPTER 4 KATIE DAVIS

Appendix B

Source trees used in Chapter 4

* Denotes a reference used for the Galliformes source data in Chapter 3.

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191 APPENDIX C: AVIAN SUPERTREE MESOZOIC BIRDS – PALAEOGNATHAE

Appendix C

Avian Supertree

192 APPENDIX C: AVIAN SUPERTREE PALAEOGNATHAE – ANSERIFORMES

193 APPENDIX C: AVIAN SUPERTREE ANSERIFORMES

194 APPENDIX C: AVIAN SUPERTREE ANSERIFORMES – GALLIFORMES

195 APPENDIX C: AVIAN SUPERTREE GALLIFORMES

196 APPENDIX C: AVIAN SUPERTREE GALLIFORMES

197 GALLIFORMES – MUSOPHAGIFORMES – PTEROCLIDIFORMES - COLUMBIFORMES

198 APPENDIX C: AVIAN SUPERTREE COLUMBIFORMES

199 APPENDIX C: AVIAN SUPERTREE COLUMBIFORMES – GRUIFORMES

200 APPENDIX C: AVIAN SUPERTREE GRUIFORMES

201 APPENDIX C: AVIAN SUPERTREE GRUIFORMES – STRIGIFORMES

202 APPENDIX C: AVIAN SUPERTREE STRIGIFORMES – FALCONIFORMES

203 APPENDIX C: AVIAN SUPERTREE FALCONIFORMES

204 APPENDIX C: AVIAN SUPERTREE FALCONIFORMES

205 PHOENICOPTERIDAE – PODICIPEDIDAE – GAVIIFORMES – SPHENISCIFORMES – PROCELLARIIFORMES

206 APPENDIX C: AVIAN SUPERTREE PROCELLARIIFORMES – PELECANIFORMES

207 APPENDIX C: AVIAN SUPERTREE PELECANIFORMES – CICONIIFORMES

208 APPENDIX C: AVIAN SUPERTREE CICONIIFORMES – TURNICIDAE

209 APPENDIX C: AVIAN SUPERTREE CHARADRIIFORMES

210 APPENDIX C: AVIAN SUPERTREE CHARADRIIFORMES

211 APPENDIX C: AVIAN SUPERTREE CHARADRIIFORMES

212 APPENDIX C: AVIAN SUPERTREE CHARADRIIFORMES

213 CHARADRIIFORMES – CUCULIFORMES – TROGONIFORMES

214 TROGONIFORMES – CAPRIMULGIFORMES – AEGOTHELIFORMES – APODIFORMES

215 APPENDIX C: AVIAN SUPERTREE APODIFORMES – TROCHILIDAE

216 APPENDIX C: AVIAN SUPERTREE TROCHILIDAE – COLIIFORMES

217 APPENDIX C: AVIAN SUPERTREE PSITTACIIFORMES

218 APPENDIX C: AVIAN SUPERTREE PSITTACIIFORMES

219 PSITTACIIFORMES – BUCEROTIFORMES – CORACIIFORMES

220 CORACIIFORMES – GALBULIFORMES - PICIFORMES

221 APPENDIX C: AVIAN SUPERTREE PICIFORMES

222 PICIFORMES – PASSERIFORMES : PITTIDAE , EURYLAIMIDAE , PHILEPITTIDAE , TYRANNIDAE , PIPRIDAE

223 PASSERIFORMES : PIPRIDAE , TITYRIDAE , OXYRUNCIDAE , COTINGIDAE

224 APPENDIX C: AVIAN SUPERTREE PASSERIFORMES : COTINGIDAE , TYRANNIDAE

225 APPENDIX C: AVIAN SUPERTREE PASSERIFORMES : TYRANNIDAE

226 PASSERIFORMES : TYRANNIDAE , CONOPOPHAGIDAE , THAMNOPHILIDAE

227 PASSERIFORMES : THAMNOPHILIDAE , FORMICARIIDAE , RHINOCRYPTIDAE

228 PASSERIFORMES : FORMICARIIDAE , FURNARIIDAE , DENDROCOLAPTIDAE

229 APPENDIX C: AVIAN SUPERTREE PASSERIFORMES : FURNARIIDAE

230 APPENDIX C: AVIAN SUPERTREE PASSERIFORMES : FURNARIIDAE

231 PASSERIFORMES : MENURIDAE , CLIMACTERIDAE , PTILONORHYNCHIDAE , MALURIDAE , PARDALOTIDAE

232 PASSERIFORMES : ACANTHIZIDAE , MELIPHAGIDAE

233 PASSERIFORMES : MELIPHAGIDAE , CNEMOPHILIDAE , MELANOCHARITIDAE , VIREONIDAE , CINCLOSOMATIDAE

234 PASSERIFORMES : CINCLOSOMATIDAE , COLLURICINCLIDAE , ORIOLIDAE , ARTAMIDAE , MALACONOTIDAE , PLATYSTEIRIDAE

235 PASSERIFORMES : VANGIDAE , DICRURIDAE , MONARCHIDAE , PARADISAEIDAE

236 PASSERIFORMES : PARADISAEIDAE , LANIIDAE , CORVIIDAE

237 PASSERIFORMES : CORVIIDAE , PETROICIDAE , REMIZIDAE , PARIDAE

238 PASSERIFORMES : PARIDAE , ALAUDIDAE , HIRUNDINIDAE , PYCNONOTIDAE

239 PASSERIFORMES : PYCNONOTIDAE , MEGALURIDAE , CISTICOLIDAE

240 PASSERIFORMES : SYLVIIDAE , ACROCEPHALIDAE , PHYLLOSCOPIDAE

241 PASSERIFORMES : PHYLLOSCOPIDAE , SYLVIIDAE , TIMALIIDAE , ZOSTEROPIDAE

242 PASSERIFORMES : ZOSTEROPIDAE , TIMALIIDAE , REGULIDAE , SITTIDAE

243 PASSERIFORMES : CERTHIDAE , POLIOPTILIDAE , TROGLODYTIDAE , BOMBYCILLIDAE , MIMIDAE

244 PASSERIFORMES : STURNIDAE , CINCLIDAE , TURDIDAE

245 PASSERIFORMES : MUSCICAPIDAE , PROMEROPIDAE

246 PASSERIFORMES : DICAEIDAE , NECTARINIIDAE , IRENIDAE , CHLOROPSEIDAE , PRUNELLIDAE , PLOCEIDAE

247 PASSERIFORMES : ESTRILIDIDAE , MOTACILLIDAE , PASSERIDAE

248 PASSERIFORMES : PASSERIDAE , FRINGILLIDAE

249 APPENDIX C: AVIAN SUPERTREE PASSERIFORMES : FRINGILLIDAE

250 PASSERIFORMES : FRINGILLIDAE , EMBERIZIDAE , CARDINALIDAE

251 PASSERIFORMES : EMBERIZIDAE , THRAUPIDAE

252 PASSERIFORMES : THRAUPIDAE , CARDINALIDAE

253 PASSERIFORMES : THRAUPIDAE , ICTERIDAE

254 PASSERIFORMES : ICTERIDAE , PARULIDAE

255 PASSERIFORMES : ICTERIDAE , EMBERIZIDAE

256 APPENDIX C: AVIAN SUPERTREE PASSERIFORMES : EMBERIZIDAE

257 APPENDIX D: SOURCES FOR CHAPTER 5 KATIE DAVIS

Appendix D

Source trees used in Chapter 5

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258 APPENDIX D: SOURCES FOR CHAPTER 5 KATIE DAVIS

and display behaviours. Biological Journal of the Linnean Society., 73:187-198. KIMBALL , R. T., E. L. B RAUN , P. W. Z WARTJES , T. M. C ROWE , AND J. D. L IGON . 1999. A molecular phylogeny of the pheasants and partridges suggests that these lineages are not monophyletic. Molecular Phylogenetics and Evolution, 11(1):38-54. LUCCHINI , V., J. H ÖGLUND , S. K LAUS , J. S WENSON , AND E. R ANDI . 2001. Historical biogeography and a mitochondrial DNA phylogeny of grouse and ptarmigan. Molecular Phylogenetics and Evolution, 20(1):149- 162. MUNECHIKA , I., K. N OZAWA , AND H. S UZUKI . 1999. Relationships of Syrmaticus and Phasianus by cyt-b gene array comparison. Japanese Journal of Ornithology, 47:133-138. NISHIBORI , M., M. T SUDZUKI , T. H AYASHI , Y. Y AMAMOTO , AND H. Y ASUE . 2002. Complete nucleotide sequence of the Coturnix chinensis (blue- breasted quail) mitochondorial genome and a phylogenetic analysis with related species. Journal of Heredity, 93(6):439-444. RANDI , E. 1996. A mitochondrial cytochrome b phylogeny of the Alectoris partridges. Molecular Phylogenetics and Evolution, 6:214-227. RANDI , E., AND V. L UCCHINI . 1998. Organisation and evolution of the mitochondrial DNA control region in the avian genus Alectoris . Journal of Molecular Evolution, 47:449-462. RANDI , E., V. L UCCHINI , T. A RMIJO -PREWITT , R. T. K IMBALL , E. L. B RAUN , AND J. D. L IGON . 2000. Mitochondrial DNA phylogeny and speciation in the tragopans. Auk, 117:1003-1015. RANDI , E., V. L UCCHINI , A. H ENNACHE , R. T. K IMBALL , E. L. B RAUN , AND J. D. LIGON . 2001. Evolution of the mitochondrial DNA control region and cytochrome b genes and the inference of phylogenetic relationships in the avian genus Lophura (Galliformes). Molecular Phylogenetics and Evolution, 19(2):187-201. SHIBUSAWA , M., M. N ISHIBORI , C. N ISHIDA -UMEHARA , M. T SUDZUKI , J. MASABANDA , D. K. G RIFFIN , AND Y. M ATSUDA . 2004. Karyotypic evolution in the Galliformes: An examination of the process of karyotypic evolution by comparison of the molecular cytogenetic findings with the molecular phylogeny. Animal Cytogenetics and Comparative Mapping, 106:111-119. ZINK , R. M., AND R. C. B LACKWELL . 1998. Molecular systematics of the scaled quail complex (genus Callipepla ). Auk, 115(2):394-403.

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